From 27ac7978737fee03b9db217587e46356dcbc2c05 Mon Sep 17 00:00:00 2001 From: NishiPhalke Date: Wed, 16 Aug 2023 11:29:50 -0400 Subject: [PATCH 1/8] misc features --- screen2.0/next.config.js | 11 + screen2.0/package.json | 5 +- .../app/search/ccredetails/linkedgenes.tsx | 2 +- .../src/app/search/ccredetails/queries.ts | 2 +- screen2.0/src/app/search/ccresearch.tsx | 18 +- screen2.0/src/app/search/gbview/allmotifs.ts | 5493 +++++++ .../src/app/search/gbview/biosampletracks.tsx | 226 + .../src/app/search/gbview/ccretooltip.tsx | 95 + screen2.0/src/app/search/gbview/controls.tsx | 39 + .../src/app/search/gbview/cytobandview.tsx | 91 + .../src/app/search/gbview/defaulttracks.tsx | 366 + .../src/app/search/gbview/egenetracks.tsx | 102 + .../app/search/gbview/genomebrowserview.tsx | 241 + .../src/app/search/gbview/shiftbutton.tsx | 29 + .../src/app/search/gbview/tfmotiftrack.tsx | 92 + .../src/app/search/gbview/zoombutton.tsx | 34 + screen2.0/src/app/search/page.tsx | 1 + screen2.0/src/app/search/types.ts | 1 + .../common/components/CcreAutocomplete.tsx | 138 + .../components/CelltypeAutocomplete.tsx | 117 + .../common/components/GeneAutocomplete.tsx | 198 + .../src/common/components/MainSearch.tsx | 60 +- .../src/common/components/SnpAutocomplete.tsx | 133 + screen2.0/yarn.lock | 13334 ++++++---------- 24 files changed, 12799 insertions(+), 8029 deletions(-) create mode 100644 screen2.0/src/app/search/gbview/allmotifs.ts create mode 100644 screen2.0/src/app/search/gbview/biosampletracks.tsx create mode 100644 screen2.0/src/app/search/gbview/ccretooltip.tsx create mode 100644 screen2.0/src/app/search/gbview/controls.tsx create mode 100644 screen2.0/src/app/search/gbview/cytobandview.tsx create mode 100644 screen2.0/src/app/search/gbview/defaulttracks.tsx create mode 100644 screen2.0/src/app/search/gbview/egenetracks.tsx create mode 100644 screen2.0/src/app/search/gbview/genomebrowserview.tsx create mode 100644 screen2.0/src/app/search/gbview/shiftbutton.tsx create mode 100644 screen2.0/src/app/search/gbview/tfmotiftrack.tsx create mode 100644 screen2.0/src/app/search/gbview/zoombutton.tsx create mode 100644 screen2.0/src/common/components/CcreAutocomplete.tsx create mode 100644 screen2.0/src/common/components/CelltypeAutocomplete.tsx create mode 100644 screen2.0/src/common/components/GeneAutocomplete.tsx create mode 100644 screen2.0/src/common/components/SnpAutocomplete.tsx diff --git a/screen2.0/next.config.js b/screen2.0/next.config.js index e3813530..c0a0cc97 100644 --- a/screen2.0/next.config.js +++ b/screen2.0/next.config.js @@ -41,6 +41,17 @@ const nextConfig = { trailingSlash: false, assetPrefix: assetPrefix, basePath: basePath, + + webpack: (config, { isServer }) => { + if (!isServer) { + // don't resolve 'fs' module on the client to prevent this error on build --> Error: Can't resolve 'fs' + config.resolve.fallback = { + fs: false + } + } + + return config; + } } module.exports = nextConfig diff --git a/screen2.0/package.json b/screen2.0/package.json index c5a6bad6..8616a867 100644 --- a/screen2.0/package.json +++ b/screen2.0/package.json @@ -55,12 +55,15 @@ "normalize.css": "^8.0.1", "only": "^0.0.2", "postcss": "8.4.27", + "queryz": "^0.0.3", "react": "18.2.0", "react-dom": "18.2.0", "server": "^1.0.38", "sharp": "^0.32.4", "tailwindcss": "3.3.3", - "typescript": "5.1.6" + "typescript": "5.1.6", + "umms-gb": "^3.9.13", + "uuid": "^9.0.0" }, "devDependencies": { "file-loader": "^6.2.0", diff --git a/screen2.0/src/app/search/ccredetails/linkedgenes.tsx b/screen2.0/src/app/search/ccredetails/linkedgenes.tsx index 5fd05a24..caaca989 100644 --- a/screen2.0/src/app/search/ccredetails/linkedgenes.tsx +++ b/screen2.0/src/app/search/ccredetails/linkedgenes.tsx @@ -27,7 +27,7 @@ export const LinkedGenes: React.FC<{ accession: string; assembly: string }> = ({ const { loading: loading_linked, data: data_linked } = useQuery(LINKED_GENES, { variables: { assembly, - accession, + accession: [accession], }, fetchPolicy: "cache-and-network", nextFetchPolicy: "cache-first", diff --git a/screen2.0/src/app/search/ccredetails/queries.ts b/screen2.0/src/app/search/ccredetails/queries.ts index 6aa59bf6..f3498f54 100644 --- a/screen2.0/src/app/search/ccredetails/queries.ts +++ b/screen2.0/src/app/search/ccredetails/queries.ts @@ -29,7 +29,7 @@ export const TOP_TISSUES = gql` } ` export const LINKED_GENES = gql` - query ($assembly: String!, $accession: String!) { + query ($assembly: String!, $accession: [String]!) { linkedGenesQuery(assembly: $assembly, accession: $accession) { assembly accession diff --git a/screen2.0/src/app/search/ccresearch.tsx b/screen2.0/src/app/search/ccresearch.tsx index d49f3ac8..e5a04729 100644 --- a/screen2.0/src/app/search/ccresearch.tsx +++ b/screen2.0/src/app/search/ccresearch.tsx @@ -1,5 +1,5 @@ "use client" -import React, { useEffect } from "react" +import React, { useEffect, useState } from "react" import { Tab, Tabs, Typography } from "@mui/material" import MainResultsTable from "../../common/components/MainResultsTable" import MainResultsFilters from "../../common/components/MainResultsFilters" @@ -7,13 +7,15 @@ import { CcreDetails } from "./ccredetails/ccredetails" import Grid2 from "../../common/mui-client-wrappers/Grid2" import { ReadonlyURLSearchParams, useSearchParams } from "next/navigation" import styled from "@emotion/styled" +import { GenomeBrowserView } from "./gbview/genomebrowserview" + export const StyledTab = styled(Tab)(() => ({ textTransform: "none", })) export const CcreSearch = ({ mainQueryParams, ccrerows, globals, assembly }) => { const searchParams: ReadonlyURLSearchParams = useSearchParams()! - const [value, setValue] = React.useState(searchParams.get("accession") ? 1 : 0) - + const [value, setValue] = useState(searchParams.get("accession") ? 1 : 0) + const [tabIndex, setTabIndex] = useState(0) const handleChange = (_, newValue: number) => { setValue(newValue) } @@ -35,6 +37,7 @@ export const CcreSearch = ({ mainQueryParams, ccrerows, globals, assembly }) => + {searchParams.get("accession") && } @@ -46,13 +49,18 @@ export const CcreSearch = ({ mainQueryParams, ccrerows, globals, assembly }) => - setTabIndex(val)}> + + + + {tabIndex===0 && } + {tabIndex===1 && + />} )} diff --git a/screen2.0/src/app/search/gbview/allmotifs.ts b/screen2.0/src/app/search/gbview/allmotifs.ts new file mode 100644 index 00000000..866fc4b7 --- /dev/null +++ b/screen2.0/src/app/search/gbview/allmotifs.ts @@ -0,0 +1,5493 @@ +export const MOTIFS = { + IRF1: [ + [0.323, 0.103, 0.503, 0.071], + [0.536, 0.179, 0.258, 0.028], + [0.818, 0.09, 0.058, 0.034], + [0.906, 0.0, 0.077, 0.017], + [0.182, 0.427, 0.213, 0.178], + [0.256, 0.242, 0.113, 0.39], + [0.1, 0.003, 0.898, 0.0], + [0.696, 0.3, 0.0, 0.004], + [0.837, 0.129, 0.005, 0.029], + [0.885, 0.0, 0.069, 0.046], + [0.082, 0.426, 0.46, 0.032], + [0.119, 0.292, 0.166, 0.423], + [0.422, 0.034, 0.486, 0.058], + [0.493, 0.145, 0.317, 0.045], + [0.511, 0.206, 0.151, 0.131], + [0.52, 0.098, 0.297, 0.085], + ], + HIC1: [ + [0.001, 0.022, 0.0, 0.977], + [0.06, 0.0, 0.938, 0.002], + [0.186, 0.783, 0.031, 0.0], + [0.007, 0.959, 0.002, 0.032], + [0.054, 0.934, 0.006, 0.006], + [0.261, 0.0, 0.169, 0.569], + [0.078, 0.487, 0.179, 0.255], + ], + LHX2: [ + [0.067, 0.666, 0.193, 0.074], + [0.0, 0.215, 0.0, 0.785], + [0.512, 0.446, 0.0, 0.041], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 0.003, 0.997], + [0.001, 0.018, 0.004, 0.978], + [0.988, 0.0, 0.0, 0.012], + ], + ZNF667: [ + [0.052, 0.058, 0.825, 0.064], + [0.236, 0.282, 0.331, 0.15], + [0.071, 0.083, 0.285, 0.561], + [0.074, 0.046, 0.816, 0.064], + [0.785, 0.012, 0.166, 0.037], + [0.083, 0.009, 0.902, 0.006], + [0.003, 0.936, 0.012, 0.049], + [0.028, 0.046, 0.025, 0.902], + [0.003, 0.448, 0.012, 0.537], + [0.123, 0.058, 0.12, 0.699], + [0.083, 0.028, 0.067, 0.822], + [0.758, 0.031, 0.117, 0.095], + [0.798, 0.117, 0.055, 0.031], + [0.393, 0.028, 0.518, 0.061], + [0.025, 0.043, 0.911, 0.021], + [0.077, 0.644, 0.187, 0.092], + [0.11, 0.788, 0.058, 0.043], + [0.518, 0.181, 0.086, 0.215], + [0.113, 0.712, 0.08, 0.095], + ], + ZNF341: [ + [0.008, 0.006, 0.977, 0.008], + [0.014, 0.961, 0.017, 0.009], + [0.047, 0.15, 0.053, 0.751], + [0.093, 0.309, 0.558, 0.041], + [0.027, 0.055, 0.01, 0.908], + [0.003, 0.069, 0.094, 0.834], + [0.075, 0.791, 0.088, 0.045], + [0.057, 0.685, 0.035, 0.223], + ], + TP53: [ + [0.264, 0.024, 0.526, 0.186], + [0.459, 0.0, 0.476, 0.066], + [0.017, 0.96, 0.001, 0.023], + [0.79, 0.0, 0.103, 0.106], + [0.209, 0.063, 0.019, 0.71], + [0.0, 0.004, 0.978, 0.018], + [0.055, 0.368, 0.0, 0.577], + [0.101, 0.59, 0.019, 0.289], + [0.156, 0.329, 0.136, 0.379], + [0.264, 0.177, 0.426, 0.133], + [0.251, 0.16, 0.411, 0.178], + [0.44, 0.054, 0.416, 0.09], + [0.079, 0.741, 0.153, 0.027], + [0.576, 0.225, 0.037, 0.162], + [0.269, 0.075, 0.137, 0.519], + [0.168, 0.078, 0.664, 0.09], + ], + SRF: [ + [0.258, 0.127, 0.089, 0.527], + [0.124, 0.132, 0.324, 0.419], + [0.261, 0.215, 0.293, 0.231], + [0.016, 0.968, 0.008, 0.008], + [0.0, 0.93, 0.0, 0.069], + [0.532, 0.061, 0.016, 0.39], + [0.251, 0.021, 0.017, 0.71], + [0.817, 0.009, 0.033, 0.141], + [0.131, 0.028, 0.004, 0.837], + [0.678, 0.016, 0.017, 0.29], + [0.353, 0.012, 0.061, 0.574], + [0.093, 0.0, 0.906, 0.001], + [0.032, 0.006, 0.951, 0.011], + [0.229, 0.294, 0.215, 0.262], + [0.419, 0.357, 0.109, 0.115], + [0.558, 0.077, 0.146, 0.219], + ], + SPIB: [ + [0.593, 0.068, 0.192, 0.148], + [0.602, 0.058, 0.23, 0.11], + [0.561, 0.029, 0.184, 0.227], + [0.182, 0.093, 0.697, 0.028], + [0.606, 0.102, 0.277, 0.015], + [0.088, 0.0, 0.904, 0.007], + [0.0, 0.004, 0.996, 0.0], + [0.991, 0.005, 0.001, 0.003], + [0.985, 0.0, 0.003, 0.012], + [0.052, 0.176, 0.769, 0.003], + [0.091, 0.076, 0.03, 0.803], + [0.076, 0.157, 0.738, 0.029], + ], + "NKX2-5": [ + [0.119, 0.154, 0.528, 0.2], + [0.172, 0.458, 0.144, 0.226], + [0.24, 0.026, 0.498, 0.236], + [0.247, 0.425, 0.163, 0.164], + [0.311, 0.187, 0.148, 0.353], + [0.316, 0.082, 0.427, 0.174], + [0.382, 0.249, 0.194, 0.175], + [0.147, 0.188, 0.406, 0.26], + [0.207, 0.307, 0.207, 0.279], + [0.31, 0.176, 0.316, 0.199], + [0.221, 0.319, 0.163, 0.296], + [0.087, 0.299, 0.176, 0.438], + [0.124, 0.206, 0.163, 0.507], + [0.205, 0.163, 0.216, 0.416], + [0.343, 0.07, 0.583, 0.004], + [0.987, 0.003, 0.003, 0.007], + [0.058, 0.019, 0.915, 0.007], + [0.404, 0.002, 0.021, 0.573], + [0.031, 0.002, 0.941, 0.027], + [0.055, 0.274, 0.541, 0.129], + ], + TBX5: [ + [0.195, 0.312, 0.018, 0.475], + [0.364, 0.131, 0.345, 0.16], + [0.008, 0.053, 0.099, 0.841], + [0.055, 0.745, 0.013, 0.187], + [0.615, 0.147, 0.039, 0.2], + [0.146, 0.427, 0.277, 0.149], + [0.333, 0.2, 0.078, 0.389], + [0.302, 0.273, 0.365, 0.059], + [0.547, 0.067, 0.144, 0.243], + [0.019, 0.929, 0.0, 0.052], + [0.816, 0.002, 0.081, 0.102], + [0.03, 0.834, 0.118, 0.017], + [0.168, 0.457, 0.068, 0.308], + [0.172, 0.192, 0.078, 0.558], + ], + ELK4: [ + [0.462, 0.116, 0.319, 0.103], + [0.008, 0.638, 0.097, 0.257], + [0.111, 0.0, 0.003, 0.887], + [0.002, 0.0, 0.0, 0.998], + [0.006, 0.994, 0.001, 0.0], + [0.005, 0.973, 0.0, 0.021], + [0.026, 0.021, 0.674, 0.279], + [0.053, 0.189, 0.653, 0.104], + ], + STAT3: [ + [0.082, 0.065, 0.078, 0.776], + [0.081, 0.012, 0.257, 0.649], + [0.192, 0.668, 0.07, 0.07], + [0.024, 0.748, 0.01, 0.218], + [0.313, 0.165, 0.35, 0.172], + [0.136, 0.003, 0.856, 0.005], + [0.03, 0.016, 0.819, 0.135], + [0.961, 0.028, 0.003, 0.008], + [0.964, 0.01, 0.022, 0.004], + ], + NR2F6: [ + [0.143, 0.125, 0.165, 0.567], + [0.12, 0.112, 0.629, 0.139], + [0.415, 0.123, 0.394, 0.068], + [0.484, 0.282, 0.129, 0.105], + [0.025, 0.949, 0.023, 0.003], + [0.015, 0.262, 0.028, 0.695], + [0.034, 0.196, 0.034, 0.736], + [0.007, 0.091, 0.001, 0.901], + [0.031, 0.012, 0.927, 0.03], + [0.44, 0.167, 0.271, 0.122], + [0.354, 0.392, 0.054, 0.199], + [0.05, 0.839, 0.046, 0.064], + [0.122, 0.363, 0.022, 0.493], + ], + FOXK2: [ + [0.028, 0.014, 0.014, 0.944], + [0.158, 0.004, 0.838, 0.0], + [0.003, 0.017, 0.017, 0.963], + [0.015, 0.0, 0.082, 0.903], + [0.002, 0.0, 0.126, 0.873], + [0.969, 0.007, 0.0, 0.023], + [0.0, 0.734, 0.016, 0.25], + ], + ZNF24: [ + [0.161, 0.533, 0.111, 0.195], + [0.415, 0.227, 0.193, 0.165], + [0.117, 0.311, 0.111, 0.461], + [0.172, 0.106, 0.163, 0.56], + [0.259, 0.569, 0.125, 0.047], + [0.527, 0.239, 0.131, 0.103], + [0.208, 0.089, 0.139, 0.564], + [0.056, 0.06, 0.085, 0.8], + [0.005, 0.968, 0.023, 0.004], + [0.878, 0.059, 0.037, 0.026], + [0.007, 0.149, 0.154, 0.69], + [0.059, 0.047, 0.082, 0.811], + [0.157, 0.656, 0.024, 0.163], + [0.572, 0.178, 0.178, 0.071], + [0.026, 0.091, 0.031, 0.851], + [0.036, 0.019, 0.044, 0.9], + [0.005, 0.984, 0.004, 0.007], + [0.568, 0.182, 0.149, 0.101], + ], + CEBPB: [ + [0.617, 0.049, 0.195, 0.139], + [0.0, 0.0, 0.0, 1.0], + [0.001, 0.0, 0.044, 0.955], + [0.332, 0.0, 0.286, 0.381], + [0.0, 0.998, 0.0, 0.002], + [0.65, 0.123, 0.001, 0.225], + [0.164, 0.363, 0.008, 0.466], + [0.716, 0.276, 0.0, 0.008], + [0.986, 0.001, 0.003, 0.01], + [0.021, 0.302, 0.136, 0.541], + ], + MAX: [ + [0.0, 1.0, 0.0, 0.0], + [0.96, 0.001, 0.018, 0.02], + [0.0, 0.481, 0.004, 0.515], + [0.031, 0.01, 0.96, 0.0], + [0.052, 0.154, 0.0, 0.795], + [0.0, 0.005, 0.92, 0.075], + ], + PPARG: [ + [0.098, 0.123, 0.08, 0.699], + [0.197, 0.143, 0.541, 0.119], + [0.57, 0.252, 0.129, 0.05], + [0.189, 0.72, 0.014, 0.077], + [0.05, 0.822, 0.007, 0.121], + [0.011, 0.161, 0.011, 0.816], + [0.075, 0.224, 0.037, 0.664], + [0.025, 0.061, 0.022, 0.893], + [0.132, 0.201, 0.536, 0.13], + [0.336, 0.316, 0.188, 0.159], + [0.065, 0.74, 0.043, 0.152], + [0.151, 0.727, 0.016, 0.107], + [0.063, 0.445, 0.046, 0.446], + [0.591, 0.145, 0.15, 0.114], + [0.214, 0.319, 0.335, 0.133], + [0.333, 0.09, 0.033, 0.544], + [0.196, 0.103, 0.152, 0.549], + ], + NFIA: [ + [0.057, 0.392, 0.103, 0.449], + [0.012, 0.19, 0.121, 0.677], + [0.045, 0.0, 0.847, 0.109], + [0.032, 0.063, 0.896, 0.009], + [0.286, 0.595, 0.041, 0.078], + [0.331, 0.204, 0.131, 0.334], + [0.206, 0.411, 0.171, 0.211], + [0.23, 0.209, 0.328, 0.234], + [0.187, 0.378, 0.239, 0.196], + [0.25, 0.105, 0.231, 0.413], + [0.042, 0.029, 0.746, 0.183], + [0.002, 0.93, 0.032, 0.035], + [0.0, 0.84, 0.0, 0.16], + [0.721, 0.027, 0.239, 0.013], + [0.37, 0.127, 0.454, 0.048], + ], + EPAS1: [ + [0.746, 0.021, 0.218, 0.015], + [0.002, 0.906, 0.001, 0.091], + [0.091, 0.0, 0.888, 0.021], + [0.004, 0.0, 0.004, 0.992], + [0.0, 0.0, 0.993, 0.007], + ], + JUNB: [ + [0.443, 0.231, 0.271, 0.055], + [0.0, 0.004, 0.001, 0.995], + [0.0, 0.0, 0.86, 0.14], + [0.991, 0.002, 0.0, 0.007], + [0.125, 0.375, 0.452, 0.047], + [0.0, 0.0, 0.0, 1.0], + [0.029, 0.971, 0.0, 0.0], + [0.992, 0.0, 0.008, 0.0], + [0.05, 0.31, 0.202, 0.438], + ], + PBX1: [ + [0.184, 0.032, 0.058, 0.727], + [0.002, 0.137, 0.86, 0.001], + [0.712, 0.16, 0.01, 0.118], + [0.071, 0.195, 0.361, 0.373], + [0.024, 0.001, 0.005, 0.971], + [0.016, 0.198, 0.783, 0.003], + [0.709, 0.001, 0.238, 0.053], + [0.008, 0.717, 0.053, 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+ [0.022, 0.102, 0.772, 0.104], + [0.898, 0.0, 0.005, 0.097], + [0.412, 0.027, 0.008, 0.552], + ], + ZBTB17: [ + [0.195, 0.22, 0.5, 0.085], + [0.182, 0.175, 0.484, 0.16], + [0.154, 0.124, 0.601, 0.121], + [0.198, 0.179, 0.163, 0.46], + [0.051, 0.107, 0.811, 0.031], + [0.026, 0.025, 0.898, 0.051], + [0.088, 0.08, 0.817, 0.015], + [0.009, 0.014, 0.921, 0.056], + [0.009, 0.009, 0.958, 0.024], + [0.431, 0.491, 0.016, 0.063], + [0.116, 0.021, 0.772, 0.091], + [0.024, 0.039, 0.899, 0.038], + [0.08, 0.033, 0.824, 0.063], + [0.04, 0.049, 0.873, 0.039], + [0.275, 0.513, 0.102, 0.11], + ], + ZNF260: [ + [0.018, 0.298, 0.034, 0.65], + [0.095, 0.785, 0.019, 0.101], + [0.052, 0.336, 0.034, 0.579], + [0.03, 0.029, 0.027, 0.914], + [0.026, 0.024, 0.033, 0.917], + [0.027, 0.026, 0.049, 0.898], + [0.187, 0.042, 0.096, 0.676], + [0.076, 0.197, 0.017, 0.711], + [0.859, 0.053, 0.042, 0.045], + [0.014, 0.18, 0.016, 0.79], + [0.154, 0.022, 0.661, 0.163], + [0.042, 0.002, 0.946, 0.009], + [0.003, 0.779, 0.019, 0.2], + [0.022, 0.032, 0.006, 0.941], + [0.028, 0.057, 0.886, 0.029], + [0.153, 0.697, 0.006, 0.144], + [0.809, 0.012, 0.175, 0.003], + [0.001, 0.004, 0.012, 0.982], + [0.918, 0.008, 0.026, 0.047], + [0.137, 0.101, 0.751, 0.011], + [0.003, 0.007, 0.014, 0.976], + [0.96, 0.005, 0.025, 0.011], + [0.002, 0.104, 0.016, 0.877], + [0.003, 0.004, 0.009, 0.984], + [0.0, 0.954, 0.003, 0.042], + [0.006, 0.945, 0.003, 0.046], + [0.861, 0.036, 0.055, 0.047], + [0.024, 0.148, 0.036, 0.792], + [0.094, 0.064, 0.53, 0.312], + [0.11, 0.068, 0.743, 0.08], + [0.067, 0.099, 0.064, 0.77], + [0.296, 0.048, 0.582, 0.075], + [0.057, 0.08, 0.056, 0.807], + [0.611, 0.049, 0.263, 0.077], + [0.149, 0.081, 0.156, 0.614], + [0.741, 0.076, 0.089, 0.095], + [0.093, 0.091, 0.073, 0.744], + [0.256, 0.049, 0.591, 0.104], + [0.091, 0.087, 0.076, 0.746], + [0.527, 0.086, 0.291, 0.096], + [0.078, 0.706, 0.06, 0.156], + [0.115, 0.702, 0.055, 0.129], + [0.731, 0.085, 0.06, 0.125], + [0.105, 0.623, 0.05, 0.222], + [0.685, 0.086, 0.084, 0.145], + [0.135, 0.094, 0.093, 0.678], + [0.097, 0.073, 0.066, 0.764], + [0.092, 0.073, 0.065, 0.77], + [0.09, 0.078, 0.066, 0.766], + [0.142, 0.545, 0.115, 0.197], + [0.093, 0.113, 0.049, 0.746], + [0.106, 0.092, 0.066, 0.736], + [0.213, 0.109, 0.052, 0.627], + [0.651, 0.084, 0.07, 0.195], + [0.123, 0.14, 0.071, 0.666], + [0.109, 0.618, 0.074, 0.2], + [0.131, 0.593, 0.076, 0.199], + [0.633, 0.108, 0.097, 0.162], + [0.173, 0.116, 0.42, 0.291], + [0.105, 0.15, 0.085, 0.66], + [0.123, 0.591, 0.079, 0.207], + [0.191, 0.18, 0.088, 0.541], + [0.47, 0.151, 0.129, 0.251], + [0.121, 0.293, 0.082, 0.505], + ], + ZNF490: [ + [0.218, 0.128, 0.143, 0.511], + [0.214, 0.123, 0.475, 0.189], + [0.231, 0.116, 0.477, 0.176], + [0.54, 0.111, 0.173, 0.176], + [0.214, 0.117, 0.147, 0.521], + [0.544, 0.12, 0.142, 0.194], + [0.586, 0.127, 0.112, 0.174], + [0.58, 0.122, 0.154, 0.144], + [0.39, 0.118, 0.344, 0.149], + [0.634, 0.119, 0.116, 0.131], + [0.395, 0.134, 0.301, 0.17], + [0.307, 0.159, 0.17, 0.364], + [0.172, 0.563, 0.105, 0.16], + [0.654, 0.142, 0.094, 0.11], + [0.585, 0.141, 0.08, 0.194], + [0.152, 0.101, 0.682, 0.065], + [0.751, 0.026, 0.197, 0.026], + [0.195, 0.599, 0.073, 0.133], + [0.059, 0.767, 0.024, 0.15], + [0.065, 0.735, 0.021, 0.179], + [0.629, 0.129, 0.048, 0.194], + [0.402, 0.087, 0.168, 0.342], + [0.098, 0.374, 0.204, 0.325], + [0.232, 0.043, 0.336, 0.39], + [0.39, 0.016, 0.537, 0.057], + [0.008, 0.046, 0.05, 0.896], + [0.284, 0.236, 0.274, 0.206], + [0.006, 0.002, 0.001, 0.991], + [0.001, 0.001, 0.97, 0.029], + [0.002, 0.811, 0.005, 0.182], + [0.004, 0.035, 0.002, 0.958], + [0.01, 0.001, 0.978, 0.011], + [0.012, 0.487, 0.046, 0.455], + [0.214, 0.506, 0.021, 0.259], + [0.064, 0.048, 0.083, 0.805], + [0.32, 0.134, 0.099, 0.447], + [0.046, 0.859, 0.033, 0.062], + [0.752, 0.136, 0.037, 0.075], + [0.553, 0.057, 0.279, 0.11], + [0.074, 0.09, 0.749, 0.087], + [0.749, 0.065, 0.111, 0.074], + [0.291, 0.082, 0.52, 0.107], + [0.706, 0.131, 0.065, 0.097], + [0.08, 0.71, 0.09, 0.121], + [0.204, 0.407, 0.078, 0.31], + [0.136, 0.583, 0.104, 0.177], + [0.662, 0.098, 0.11, 0.13], + [0.118, 0.33, 0.103, 0.45], + [0.112, 0.481, 0.097, 0.31], + [0.123, 0.109, 0.096, 0.671], + [0.185, 0.488, 0.109, 0.218], + [0.651, 0.114, 0.116, 0.118], + [0.161, 0.461, 0.132, 0.247], + [0.389, 0.217, 0.244, 0.149], + [0.134, 0.173, 0.122, 0.571], + ], + ZBTB26: [ + [0.012, 0.041, 0.141, 0.806], + [0.003, 0.984, 0.01, 0.004], + [0.013, 0.539, 0.08, 0.368], + [0.467, 0.033, 0.485, 0.014], + [0.006, 0.005, 0.985, 0.004], + [0.883, 0.034, 0.052, 0.03], + [0.506, 0.097, 0.264, 0.132], + ], + TAL1: [ + [0.075, 0.5, 0.219, 0.206], + [0.053, 0.048, 0.005, 0.894], + [0.098, 0.0, 0.0, 0.902], + [1.0, 0.0, 0.0, 0.0], + [0.001, 0.0, 0.0, 0.999], + [0.0, 1.0, 0.0, 0.0], + [0.321, 0.013, 0.017, 0.649], + ], + ELF2: [ + [0.514, 0.082, 0.269, 0.134], + [0.011, 0.777, 0.098, 0.114], + [0.036, 0.0, 0.0, 0.964], + [0.001, 0.0, 0.003, 0.996], + [0.0, 0.971, 0.013, 0.016], + [0.009, 0.97, 0.0, 0.022], + [0.026, 0.025, 0.611, 0.338], + [0.032, 0.228, 0.638, 0.102], + ], + NANOG: [ + [0.05, 0.485, 0.191, 0.274], + [0.084, 0.459, 0.107, 0.349], + [0.43, 0.051, 0.06, 0.459], + [0.023, 0.042, 0.033, 0.902], + [0.074, 0.007, 0.035, 0.884], + [0.092, 0.299, 0.553, 0.056], + [0.353, 0.015, 0.062, 0.57], + [0.254, 0.246, 0.141, 0.358], + [0.742, 0.039, 0.083, 0.136], + [0.048, 0.045, 0.05, 0.857], + [0.013, 0.007, 0.754, 0.226], + [0.037, 0.547, 0.127, 0.289], + [0.615, 0.021, 0.084, 0.281], + [0.651, 0.031, 0.191, 0.127], + [0.737, 0.054, 0.089, 0.121], + [0.165, 0.143, 0.167, 0.524], + ], + ONECUT2: [ + [0.145, 0.115, 0.057, 0.683], + [0.994, 0.001, 0.003, 0.002], + [0.148, 0.012, 0.014, 0.826], + [0.228, 0.002, 0.089, 0.68], + [0.0, 0.0, 1.0, 0.0], + [0.961, 0.01, 0.026, 0.003], + [0.017, 0.04, 0.016, 0.927], + [0.019, 0.071, 0.041, 0.869], + [0.23, 0.081, 0.076, 0.614], + ], + GLIS3: [ + [0.409, 0.198, 0.393, 0.0], + [0.023, 0.834, 0.003, 0.14], + [0.002, 0.971, 0.009, 0.018], + [0.102, 0.622, 0.002, 0.274], + [0.0, 0.997, 0.0, 0.002], + [0.103, 0.887, 0.003, 0.006], + [0.158, 0.526, 0.01, 0.306], + [0.393, 0.004, 0.578, 0.025], + [0.01, 0.759, 0.222, 0.009], + [0.356, 0.216, 0.24, 0.189], + [0.218, 0.139, 0.468, 0.176], + [0.405, 0.188, 0.275, 0.132], + [0.011, 0.163, 0.761, 0.065], + ], + ZFX: [ + [0.145, 0.484, 0.07, 0.301], + [0.119, 0.348, 0.325, 0.208], + [0.389, 0.133, 0.41, 0.068], + [0.001, 0.0, 0.985, 0.015], + [0.002, 0.0, 0.992, 0.006], + [0.006, 0.993, 0.0, 0.001], + [0.0, 0.998, 0.0, 0.002], + [0.005, 0.076, 0.0, 0.919], + [0.245, 0.209, 0.365, 0.181], + [0.054, 0.384, 0.454, 0.109], + ], + RBPJ: [ + [0.006, 0.212, 0.015, 0.767], + [0.0, 0.003, 0.0, 0.996], + [0.0, 1.0, 0.0, 0.0], + [0.063, 0.741, 0.0, 0.196], + [0.001, 0.987, 0.011, 0.0], + [0.775, 0.0, 0.188, 0.037], + [0.023, 0.437, 0.375, 0.165], + [0.257, 0.254, 0.407, 0.083], + [0.236, 0.35, 0.372, 0.042], + ], + ZNF680: [ + [0.198, 0.036, 0.711, 0.055], + [0.295, 0.184, 0.259, 0.262], + [0.09, 0.764, 0.03, 0.116], + [0.309, 0.564, 0.026, 0.102], + [0.792, 0.01, 0.166, 0.032], + [0.672, 0.005, 0.253, 0.07], + [0.001, 0.001, 0.998, 0.0], + [0.998, 0.001, 0.001, 0.0], + [0.946, 0.003, 0.035, 0.016], + [0.161, 0.002, 0.828, 0.009], + [0.996, 0.002, 0.002, 0.0], + [0.472, 0.288, 0.039, 0.201], + [0.041, 0.152, 0.03, 0.776], + [0.291, 0.138, 0.258, 0.312], + [0.626, 0.086, 0.077, 0.211], + [0.3, 0.036, 0.598, 0.067], + ], + } + \ No newline at end of file diff --git a/screen2.0/src/app/search/gbview/biosampletracks.tsx b/screen2.0/src/app/search/gbview/biosampletracks.tsx new file mode 100644 index 00000000..cadc0e35 --- /dev/null +++ b/screen2.0/src/app/search/gbview/biosampletracks.tsx @@ -0,0 +1,226 @@ +import { gql, useQuery } from "@apollo/client"; +import { associateBy } from "queryz"; +import { BigWigData, BigBedData, BigZoomData } from "bigwig-reader"; +import React, { RefObject, useEffect, useMemo, useState } from "react"; +import { DenseBigBed, EmptyTrack, FullBigWig } from "umms-gb"; +import { + BigRequest, + RequestError, +} from "umms-gb/dist/components/tracks/trackset/types"; +import { ValuedPoint } from "umms-gb/dist/utils/types"; +import { client } from "../ccredetails/client" +import CCRETooltip from "./ccretooltip" +import { TitledTrack } from "./defaulttracks"; + +type GenomicRange = { + chromosome?: string; + start: number; + end: number; + }; + +type BiosampleTracksProps = { + tracks: [string, string, string][]; + biosample: string; + domain: GenomicRange; + onHeightChanged?: (i: number) => void; + cCREHighlight?: GenomicRange; + cCREHighlights?: Set; + svgRef?: RefObject; + assembly: string; + oncCREClicked?: (accession: string) => void; + oncCREMousedOver?: (coordinates?: GenomicRange) => void; + oncCREMousedOut?: () => void; + onSettingsClick?: () => void; + }; + + + +export type BigResponseData = + | BigWigData[] + | BigBedData[] + | BigZoomData[] + | ValuedPoint[]; + +export type BigResponse = { + data: BigResponseData; + error: RequestError; +}; + +export type BigQueryResponse = { + bigRequests: BigResponse[]; +}; +export const BIG_QUERY = gql` + query BigRequests($bigRequests: [BigRequest!]!) { + bigRequests(requests: $bigRequests) { + data + error { + errortype + message + } + } + } +`; + +export const COLOR_MAP : Map = + new Map([ + [ + "DNase", + "#06da93" + + ], + [ + "H3K4me3", + "#ff0000" + + ] + , + [ + "H3K27ac", + "#ffcd00" + + ], + [ + "CTCF", + "#00b0d0" + + ] + ]); + + export const BIOSAMPLE_QUERY = gql` + query q ($assembly: String!) { + ccREBiosampleQuery(assembly: $assembly) { + biosamples { + name + dnase: experimentAccession(assay: "DNase") + h3k4me3: experimentAccession(assay: "H3K4me3") + h3k27ac: experimentAccession(assay: "H3K27ac") + ctcf: experimentAccession(assay: "CTCF") + dnase_signal: fileAccession(assay: "DNase") + h3k4me3_signal: fileAccession(assay: "H3K4me3") + h3k27ac_signal: fileAccession(assay: "H3K27ac") + ctcf_signal: fileAccession(assay: "CTCF") + } + } + } + ` +export const BiosampleTracks:React.FC = (props) => { + const [cTracks, setTracks] = useState<[string, string, string][]>(props.tracks) + + useEffect(()=>{ + setTracks(props.tracks) + },[props.tracks]) + const height = useMemo(() => cTracks && cTracks.length * 80, [cTracks]); + const bigRequests = useMemo( + () => + cTracks && cTracks.map((x) => ({ + chr1: props.domain.chromosome!, + start: props.domain.start, + end: props.domain.end, + preRenderedWidth: 1400, + url: x[1], + })), + [cTracks, props] + ); + const { data, loading } = useQuery(BIG_QUERY, { + variables: { bigRequests }, + client, + skip: bigRequests===null + + }); + const { data: biosampleData, loading: biosampleDataLoading } = useQuery(BIOSAMPLE_QUERY, { + variables: { assembly: "grch38" }, + client + }); + const groupedBiosamples = useMemo( + () => + associateBy( + biosampleData && biosampleData.ccREBiosampleQuery ? biosampleData.ccREBiosampleQuery.biosamples : [], + (x: any) => x.name as any, + (x) => x + ), + [biosampleData,biosampleDataLoading] + ) + console.log(groupedBiosamples.get(props.biosample)) + const cCRECoordinateMap = useMemo( + () => + associateBy( + (data && data.bigRequests && data.bigRequests[0].data) || [], + (x) => x.name, + (x) => ({ chromosome: x.chr, start: x.start, end: x.end }) + ), + [data] + ) + useEffect(() => { + height && props.onHeightChanged && props.onHeightChanged(height); + }, [props.onHeightChanged, height, props]); + + const [settingsMousedOver, setSettingsMousedOver] = useState(false); + const [settingsModalShown, setSettingsModalShown] = useState(false); + + return loading || !cTracks || !height || (data?.bigRequests.length || 0) < 2 ? ( + + ) : ( + <> + + + + {(data?.bigRequests || []).map((data, i) => ( + + ))} + + + + {settingsMousedOver && ( + + )} + + setSettingsMousedOver(true)} + onMouseOut={() => setSettingsMousedOver(false)} + strokeWidth={1} + transform="translate(20,0)" + onClick={() => { + props.onSettingsClick && props.onSettingsClick(); + setSettingsModalShown(true); + }} + /> + + Biosample-Specific Tracks + + + ); +} \ No newline at end of file diff --git a/screen2.0/src/app/search/gbview/ccretooltip.tsx b/screen2.0/src/app/search/gbview/ccretooltip.tsx new file mode 100644 index 00000000..b8475ff1 --- /dev/null +++ b/screen2.0/src/app/search/gbview/ccretooltip.tsx @@ -0,0 +1,95 @@ +import { gql, useQuery } from "@apollo/client" +import React, { useMemo } from "react" +import { CircularProgress } from "@mui/material" +import { client } from "../ccredetails/client" + +export const COLORS = new Map([ + ["PLS", "#ff0000"], + ["pELS", "#ffa700"], + ["dELS", "#ffcd00"], + ["DNase-H3K4me3", "#ffaaaa"], + ["CTCF-only", "#00b0f0"], +]) + +export const GROUPS = new Map([ + ["PLS", "promoter-like"], + ["pELS", "proximal enhancer-like"], + ["dELS", "distal enhancer-like"], + ["DNase-H3K4me3", "DNase-H3K4me3"], + ["CTCF-only", "CTCF-only"], +]) + +const QUERY = gql` + query cCRE($assembly: String!, $accession: [String!], $experiments: [String!]) { + cCREQuery(assembly: $assembly, accession: $accession) { + group + zScores(experiments: $experiments) { + experiment + score + } + } + } +` + +const MAXZ_QUERY = gql` + query cCRE($assembly: String!, $accession: [String!]) { + cCREQuery(assembly: $assembly, accession: $accession) { + group + dnase: maxZ(assay: "dnase") + h3k4me3: maxZ(assay: "h3k4me3") + h3k27ac: maxZ(assay: "h3k27ac") + ctcf: maxZ(assay: "ctcf") + } + } +` + +const biosampleExperiments = (x) => [x.dnase, x.h3k4me3, x.h3k27ac, x.ctcf].filter((xx) => !!xx) + +const MARKS = ["DNase", "H3K4me3", "H3K27ac", "CTCF"] +const marks = (x) => [x.dnase, x.h3k4me3, x.h3k27ac, x.ctcf].map((x, i) => x && MARKS[i]).filter((xx) => !!xx) + +const CCRETooltip = (props) => { + const experiments = useMemo( + () => (props.biosample ? biosampleExperiments(props.biosample) : ["dnase", "h3k4me3", "h3k27ac", "ctcf"]), + [props] + ) + const { data, loading } = useQuery(props.biosample ? QUERY : MAXZ_QUERY, { + variables: { + assembly: props.assembly, + accession: props.name, + experiments, + }, + client + }) + return ( +
+ {loading || !data.cCREQuery[0] ? ( + + ) : ( + <> + + + + {props.name} ⸱ {GROUPS.get(data.cCREQuery[0].group || "")} + + + Click for details about this cCRE +
+
+ {props.biosample ? "Z-scores in " + props.biosample.name : "Max Z-scores across all biosamples:"} +
+ {(props.biosample ? marks(props.biosample) : MARKS).map((x, i) => ( + + {x}:{" "} + {props.biosample + ? data.cCREQuery[0].zScores.find((xx) => xx.experiment === experiments[i]).score.toFixed(2) + : data.cCREQuery[0][experiments[i]].toFixed(2)} +
+ + ))} + + )} +
+ ) +} +export default CCRETooltip diff --git a/screen2.0/src/app/search/gbview/controls.tsx b/screen2.0/src/app/search/gbview/controls.tsx new file mode 100644 index 00000000..144ceb90 --- /dev/null +++ b/screen2.0/src/app/search/gbview/controls.tsx @@ -0,0 +1,39 @@ +import React from 'react'; + +import ShiftButton from './shiftbutton'; +import ZoomButton from './zoombutton'; + +export interface Domain { + chromosome?: string; + start: number; + end: number; +}; +export type ControlProps = { + domain: Domain; + onDomainChanged: (domain: Domain) => void; + +}; +const Controls = ({ domain, onDomainChanged }) => { + return( + <> + move  + + + + + +   + zoom in  + + +   + zoom out  + + + + + +
+ +)}; +export default Controls; \ No newline at end of file diff --git a/screen2.0/src/app/search/gbview/cytobandview.tsx b/screen2.0/src/app/search/gbview/cytobandview.tsx new file mode 100644 index 00000000..0bfa6902 --- /dev/null +++ b/screen2.0/src/app/search/gbview/cytobandview.tsx @@ -0,0 +1,91 @@ +import React, { useMemo } from "react"; +import { gql, useQuery } from "@apollo/client"; +import { Cytobands } from "umms-gb"; +import { Grid } from "@mui/material"; +import { client } from "../ccredetails/client" +export type GenomicRange = { + chromosome?: string; + start: number; + end: number; + }; + +const CYTOBAND_QUERY = gql` + query cytobands($assembly: String!, $chromosome: String) { + cytoband(assembly: $assembly, chromosome: $chromosome) { + stain + coordinates { + chromosome + start + end + } + } + } +`; + +export type CytobandQueryResponse = { + cytoband: { + stain: string; + coordinates: { + chromosome: string; + start: number; + end: number; + }; + }[]; +}; + +export type CytobandsProps = { + assembly: string; + chromosome: string; + innerWidth: number; + height: number; + position?: GenomicRange; +}; + +const CytobandView: React.FC = (props) => { + const { loading, data } = useQuery(CYTOBAND_QUERY, { + variables: { + assembly: props.assembly, + chromosome: props.chromosome, + }, + fetchPolicy: "cache-and-network", + nextFetchPolicy: "cache-first", + client, + }); + const domain = useMemo( + () => + data && { + start: 0, + end: Math.max( + ...(data.cytoband.length === 0 + ? [1] + : data.cytoband.map((x) => x.coordinates.end)) + ), + }, + [data] + ); + return loading || !data ? null : ( + + + + + + + + + + {props.assembly}:{props.chromosome} + + + + ); +}; +export default CytobandView; diff --git a/screen2.0/src/app/search/gbview/defaulttracks.tsx b/screen2.0/src/app/search/gbview/defaulttracks.tsx new file mode 100644 index 00000000..1a9827e0 --- /dev/null +++ b/screen2.0/src/app/search/gbview/defaulttracks.tsx @@ -0,0 +1,366 @@ +import { gql, useQuery } from "@apollo/client"; +import { associateBy } from "queryz" +import { BigWigData, BigBedData, BigZoomData } from "bigwig-reader"; +import React, { RefObject, useEffect, useMemo, useState } from "react"; +import { DenseBigBed, EmptyTrack, FullBigWig } from "umms-gb"; +import { + BigRequest, + RequestError, +} from "umms-gb/dist/components/tracks/trackset/types"; +import { ValuedPoint } from "umms-gb/dist/utils/types"; +import { client } from "../ccredetails/client" +import CCRETooltip from "./ccretooltip" +/* +export const DEFAULT_TRACKS = ( + assembly: string +): Map => { + console.log +return assembly.toLowerCase() === "mm10" + ? new Map([ + ["All cCREs colored by group", { url: `gs://gcp.wenglab.org/${assembly}-cCREs.bigBed` }], + ["Aggregated DNase-seq signal, all Registry biosamples", { url: `gs://gcp.wenglab.org/dnase.${assembly}.sum.bigWig` }], + ]) : + new Map([ + [ + "All cCREs colored by group", + { + url: "gs://gcp.wenglab.org/GRCh38-cCREs.bigBed", + }, + ], + [ + "Aggregated DNase-seq signal, all Registry biosamples", + { + url: "gs://gcp.wenglab.org/dnase.GRCh38.sum.bigWig", + }, + ], + [ + "Aggregated H3K4me3 ChIP-seq signal, all Registry biosamples", + { + url: "gs://gcp.wenglab.org/h3k4me3.hg38.sum.bigWig", + }, + ] + , + [ + "Aggregated H3K27ac ChIP-seq signal, all Registry biosamples", + { + url: "gs://gcp.wenglab.org/h3k27ac.hg38.sum.bigWig", + }, + ], + [ + "Aggregated CTCF ChIP-seq signal, all Registry biosamples", + { + url: "gs://gcp.wenglab.org/ctcf.hg38.sum.bigWig", + }, + ] + + ]); +} + +export const TRACK_ORDER = (assembly) => {return assembly.toLowerCase() === "mm10" ? [ "All cCREs colored by group", +"Aggregated DNase-seq signal, all Registry biosamples"] +:[ + "All cCREs colored by group", + "Aggregated DNase-seq signal, all Registry biosamples", + "Aggregated H3K4me3 ChIP-seq signal, all Registry biosamples", + "Aggregated H3K27ac ChIP-seq signal, all Registry biosamples", + "Aggregated CTCF ChIP-seq signal, all Registry biosamples" + +]}; + +export const tracks = (assembly: string, pos: GenomicRange) => + TRACK_ORDER(assembly).map((x) => ({ + chr1: pos.chromosome!, + start: pos.start, + end: pos.end, + ...DEFAULT_TRACKS(assembly).get(x)!, + preRenderedWidth: 1400, + })); +*/ +export const BIG_QUERY = gql` + query BigRequests($bigRequests: [BigRequest!]!) { + bigRequests(requests: $bigRequests) { + data + error { + errortype + message + } + } + } +`; + +export const COLOR_MAP : Map = + new Map([ + [ + "Aggregated DNase-seq signal, all Registry biosamples", + "#06da93" + + ], + [ + "Aggregated H3K4me3 ChIP-seq signal, all Registry biosamples", + "#ff0000" + + ] + , + [ + "Aggregated H3K27ac ChIP-seq signal, all Registry biosamples", + "#ffcd00" + + ], + [ + "Aggregated CTCF ChIP-seq signal, all Registry biosamples", + "#00b0d0" + + ] + ]); + +type GenomicRange = { + chromosome?: string; + start: number; + end: number; +}; + +export type BigResponseData = + | BigWigData[] + | BigBedData[] + | BigZoomData[] + | ValuedPoint[]; + +export type BigResponse = { + data: BigResponseData; + error: RequestError +}; + +export type BigQueryResponse = { + bigRequests: BigResponse[]; +}; + +type DefaultTracksProps = { + //tracks: BigRequest[]; + domain: GenomicRange; + onHeightChanged?: (i: number) => void; + cCREHighlight?: GenomicRange; + cCREHighlights?: Set; + svgRef?: RefObject; + assembly: string; + oncCREClicked?: (accession: string) => void; + oncCREMousedOver?: (coordinates?: GenomicRange) => void; + oncCREMousedOut?: () => void; + onSettingsClick?: () => void; +}; + +export const TitledTrack: React.FC<{ + data: BigResponseData; + assembly: string; + url: string; + title: string; + color?: string; + height: number; + transform?: string; + onHeightChanged?: (height: number) => void; + domain: GenomicRange; + svgRef?: React.RefObject; + oncCREMousedOver?: (coordinates?: GenomicRange) => void; + oncCREMousedOut?: () => void; + cCRECoordinateMap?: any; + biosample?: string +}> = ({ + data, + assembly, + url, + title, + height, + domain, + transform, + onHeightChanged, + svgRef, + color, + oncCREMousedOver, + oncCREMousedOut, + cCRECoordinateMap, + biosample +}) => { + useEffect( + () => onHeightChanged && onHeightChanged(height + 40), + [height, onHeightChanged] + ); + console.log(color,title) + return ( + + + {(url.endsWith(".bigBed") || url.endsWith(".bigbed")) ? ( + } + onMouseOver={(x) => oncCREMousedOver && x.name && oncCREMousedOver(cCRECoordinateMap.get(x.name))} + onMouseOut={oncCREMousedOut} + /> + ) : ( + + )} + + ); +}; + +const DefaultTracks: React.FC = (props) => { + + const [cTracks, setTracks] = useState<[string, string][]>( props.assembly.toLowerCase()==='mm10' ? [ + [ + "All cCREs colored by group", + "gs://gcp.wenglab.org/mm10-cCREs.bigBed", + + ], + [ + "Aggregated DNase-seq signal, all Registry biosamples", + "gs://gcp.wenglab.org/dnase.mm10.sum.bigWig", + + + ], + ] : [ + [ + "All cCREs colored by group", + "gs://gcp.wenglab.org/GRCh38-cCREs.bigBed", + + ], + [ + "Aggregated DNase-seq signal, all Registry biosamples", + "gs://gcp.wenglab.org/dnase.GRCh38.sum.bigWig", + + ], + [ + "Aggregated H3K4me3 ChIP-seq signal, all Registry biosamples", + "gs://gcp.wenglab.org/h3k4me3.hg38.sum.bigWig", + + ] + , + [ + "Aggregated H3K27ac ChIP-seq signal, all Registry biosamples", + "gs://gcp.wenglab.org/h3k27ac.hg38.sum.bigWig", + + ], + [ + "Aggregated CTCF ChIP-seq signal, all Registry biosamples", + "gs://gcp.wenglab.org/ctcf.hg38.sum.bigWig", + + ] + ]); + const height = useMemo(() => cTracks.length * 80, [cTracks]); + const bigRequests = useMemo( + () => + cTracks.map((x) => ({ + chr1: props.domain.chromosome!, + start: props.domain.start, + end: props.domain.end, + preRenderedWidth: 1400, + url: x[1], + })), + [cTracks, props] + ); + const { data, loading } = useQuery(BIG_QUERY, { + variables: { bigRequests }, + client + }); + const cCRECoordinateMap = useMemo( + () => + associateBy( + (data && data.bigRequests && data.bigRequests[0].data) || [], + (x) => x.name, + (x) => ({ chromosome: x.chr, start: x.start, end: x.end }) + ), + [data] + ) + useEffect(() => { + props.onHeightChanged && props.onHeightChanged(height); + }, [props.onHeightChanged, height, props]); + + const [settingsMousedOver, setSettingsMousedOver] = useState(false); + const [settingsModalShown, setSettingsModalShown] = useState(false); + + return loading || (data?.bigRequests.length || 0) < 2 ? ( + + ) : ( + <> + + + + {(data?.bigRequests || []).map((data, i) => ( + + ))} + + + + {settingsMousedOver && ( + + )} + + setSettingsMousedOver(true)} + onMouseOut={() => setSettingsMousedOver(false)} + strokeWidth={1} + transform="translate(20,0)" + onClick={() => { + props.onSettingsClick && props.onSettingsClick(); + setSettingsModalShown(true); + }} + /> + + Aggregated signal Tracks + + + ); +}; +export default DefaultTracks; diff --git a/screen2.0/src/app/search/gbview/egenetracks.tsx b/screen2.0/src/app/search/gbview/egenetracks.tsx new file mode 100644 index 00000000..1765673c --- /dev/null +++ b/screen2.0/src/app/search/gbview/egenetracks.tsx @@ -0,0 +1,102 @@ + +import React, { useState } from "react"; +import { + EmptyTrack, + PackTranscriptTrack, + SquishTranscriptTrack, +} from "umms-gb"; +import { TranscriptList } from "umms-gb/dist/components/tracks/transcripts/types"; + +export type GenomicRange = { + chromosome?: string; + start: number; + end: number; +}; +export type EGeneTrackProps = { + expandedCoordinates: GenomicRange; + genes: TranscriptList[]; + highlights?: Set; + onSettingsClick?: () => void; + onHeightChanged?: (x: number) => void; + width?: number; + squish?: boolean; +}; + +const EGeneTracks: React.FC = (props) => { + const [settingsMousedOver, setSettingsMousedOver] = useState(false); + const [height, setHeight] = useState(60); + return ( + + + {props.squish ? ( + { + setHeight(x + 40); + props.onHeightChanged && props.onHeightChanged(40 + x); + }} + color="#880000" + /> + ) : ( + { + setHeight(x + 40); + props.onHeightChanged && props.onHeightChanged(40 + x); + }} + color="#880000" + /> + )} + {settingsMousedOver && ( + + )} + + setSettingsMousedOver(true)} + onMouseOut={() => setSettingsMousedOver(false)} + strokeWidth={1} + transform="translate(20,0)" + onClick={props.onSettingsClick} + /> + + Genes + + + ); +}; +export default EGeneTracks; diff --git a/screen2.0/src/app/search/gbview/genomebrowserview.tsx b/screen2.0/src/app/search/gbview/genomebrowserview.tsx new file mode 100644 index 00000000..4e433de7 --- /dev/null +++ b/screen2.0/src/app/search/gbview/genomebrowserview.tsx @@ -0,0 +1,241 @@ +"use client" +import React, { useMemo, useState, useRef, useCallback, useEffect } from "react" +import Grid2 from "../../../common/mui-client-wrappers/Grid2" +import { RulerTrack, GenomeBrowser } from "umms-gb"; +import Controls from "./controls"; +import { gql, useQuery } from "@apollo/client"; +import CytobandView, { GenomicRange } from "./cytobandview" +import EGeneTracks from "./egenetracks"; +import { client } from "../ccredetails/client" +import DefaultTracks from "./defaulttracks"; +import {BiosampleTracks} from "./biosampletracks" +type GenomeBrowserViewProps = { + coordinates : { + start: number, + end: number, + chromosome?: string + }, + biosample?: string + gene?: string + assembly: string +} +const BIOSAMPLE_QUERY = gql` +query biosamples { + human: ccREBiosampleQuery(assembly: "grch38") { + biosamples { + name + dnase: experimentAccession(assay: "DNase") + h3k4me3: experimentAccession(assay: "H3K4me3") + h3k27ac: experimentAccession(assay: "H3K27ac") + ctcf: experimentAccession(assay: "CTCF") + dnase_signal: fileAccession(assay: "DNase") + h3k4me3_signal: fileAccession(assay: "H3K4me3") + h3k27ac_signal: fileAccession(assay: "H3K27ac") + ctcf_signal: fileAccession(assay: "CTCF") + } + } + mouse: ccREBiosampleQuery(assembly: "mm10") { + biosamples { + name + dnase: experimentAccession(assay: "DNase") + h3k4me3: experimentAccession(assay: "H3K4me3") + h3k27ac: experimentAccession(assay: "H3K27ac") + ctcf: experimentAccession(assay: "CTCF") + dnase_signal: fileAccession(assay: "DNase") + h3k4me3_signal: fileAccession(assay: "H3K4me3") + h3k27ac_signal: fileAccession(assay: "H3K27ac") + ctcf_signal: fileAccession(assay: "CTCF") + } + } +} +` +const GENE_QUERY = gql` + query s( + $chromosome: String + $start: Int + $end: Int + $assembly: String! + ) { + + gene( + chromosome: $chromosome + start: $start + end: $end + assembly: $assembly + ) { + name + strand + transcripts { + name + strand + exons { + coordinates { + chromosome + start + end + } + } + coordinates { + chromosome + start + end + } + } + } + } +`; +export type Transcript = { + id: string; + name: string; + strand: string; + coordinates: GenomicRange; +}; +export type SNPQueryResponse = { + gene: { + name: string; + strand: string; + transcripts: Transcript[]; + }[]; +}; +export function expandCoordinates(coordinates, l = 20000) { + return { + chromosome: coordinates.chromosome, + start: coordinates.start - l < 0 ? 0 : coordinates.start - l, + end: coordinates.end + l, + } + } + +export const GenomeBrowserView: React.FC = (props) =>{ + console.log(props.gene) + const svgRef = useRef(null); + const expandedCoordinates = useMemo(() => expandCoordinates(props.coordinates), [props.coordinates]) + const [coordinates, setCoordinates] = useState(expandedCoordinates); + const [highlight, setHighlight] = useState(null) + const [cTracks, setTracks] = useState<[string, string, string][]| null>(null) + const snpResponse = useQuery(GENE_QUERY, { + variables: { ...coordinates, assembly:props.assembly }, + fetchPolicy: "cache-and-network", + nextFetchPolicy: "cache-first", + client, + }); + + const groupedTranscripts = useMemo( + () => + snpResponse.data?.gene.map((x) => ({ + ...x, + transcripts: x.transcripts.map((xx) => ({ + ...xx, + color: props.gene ? (x).name.includes(props.gene) ? "#880000" : "#aaaaaa" : "#aaaaaa" + })), + })), + [snpResponse,props.gene] + ); + const onDomainChanged = useCallback( + (d: GenomicRange) => { + const chr = + d.chromosome === undefined + ? props.coordinates.chromosome + : d.chromosome; + const start = Math.round(d.start); + const end = Math.round(d.end); + if (end - start > 10) { + setCoordinates({ chromosome: chr, start, end }); + } + }, + [props.coordinates] + ); + const l = useCallback((c) => ((c - coordinates.start) * 1400) / (coordinates.end - coordinates.start), [coordinates]) + + const { loading: bloading, data : bdata } = useQuery(BIOSAMPLE_QUERY, { + fetchPolicy: "cache-and-network", + nextFetchPolicy: "cache-first", + client, + }); + useEffect(()=>{ + if(bdata && props.biosample) + { + const humanBiosamples = bdata && bdata.human && bdata.human.biosamples + const mouseBiosamples = bdata && bdata.mouse && bdata.mouse.biosamples + + const result = props.assembly==="mm10" ? mouseBiosamples.find(m=>m.name===props.biosample) : humanBiosamples.find(m=>m.name===props.biosample) + const r = [result.dnase_signal, result.h3k4me3_signal, result.h3k27ac_signal, result.ctcf_signal].filter((x) => !!x) + //copy v4 bed files to google bucket + const bigBedUrl = `https://downloads.wenglab.org/Registry-V4/${r.join("_")}.bigBed` + let tracks:[string, string, string][] = [[`cCREs colored by activity in ${props.biosample}`,bigBedUrl ,""]] + if(result.dnase_signal) tracks.push([`DNase-seq signal in ${props.biosample}`,`https://www.encodeproject.org/files/${result.dnase_signal}/@@download/${result.dnase_signal}.bigWig`,"DNase"]) + if(result.h3k4me3_signal) tracks.push([`H3K4me3 ChIP-seq signal in ${props.biosample}`,`https://www.encodeproject.org/files/${result.h3k4me3_signal}/@@download/${result.h3k4me3_signal}.bigWig`,"H3K4me3"]) + if(result.h3k27ac_signal) tracks.push([`H3K27ac ChIP-seq signal in ${props.biosample}`,`https://www.encodeproject.org/files/${result.h3k27ac_signal}/@@download/${result.h3k27ac_signal}.bigWig`,"H3K27ac"]) + if(result.ctcf_signal) tracks.push([`CTCF ChIP-seq signal in ${props.biosample}`,`https://www.encodeproject.org/files/${result.ctcf_signal}/@@download/${result.ctcf_signal}.bigWig`,"CTCF"]) + setTracks(tracks) + + } + + },[bdata,props.biosample]) + return(<> + +
+ +
+
+ +
+
+
+ { + if (Math.ceil(x.end) - Math.floor(x.start) > 10) { + setCoordinates({ + chromosome: coordinates.chromosome, + start: Math.floor(x.start), + end: Math.ceil(x.end), + }); + } + }} + > + {highlight && ( + + )} + + = 500000 ? true: false } + /> + + x && setHighlight(x)} + oncCREMousedOut={() => setHighlight(null)} + /> + {props.biosample && props.assembly!="mm10" && cTracks && x && setHighlight(x)} + oncCREMousedOut={() => setHighlight(null)} + />} + + + + ) +} \ No newline at end of file diff --git a/screen2.0/src/app/search/gbview/shiftbutton.tsx b/screen2.0/src/app/search/gbview/shiftbutton.tsx new file mode 100644 index 00000000..dc20d4b6 --- /dev/null +++ b/screen2.0/src/app/search/gbview/shiftbutton.tsx @@ -0,0 +1,29 @@ +import React from 'react'; +import { + Button + } from "@mui/material" +export interface Domain { + chromosome?: string; + start: number; + end: number; +}; + +export type ShiftButtonProps = { + text: string; + shift: number; + domain: Domain; + onClick: (domain: Domain) => void; +}; + +const ShiftButton= ({ text, shift, domain, onClick }) => { + return ( + <> + + + +)}; +export default ShiftButton; \ No newline at end of file diff --git a/screen2.0/src/app/search/gbview/tfmotiftrack.tsx b/screen2.0/src/app/search/gbview/tfmotiftrack.tsx new file mode 100644 index 00000000..48608674 --- /dev/null +++ b/screen2.0/src/app/search/gbview/tfmotiftrack.tsx @@ -0,0 +1,92 @@ +import React, { useState, useRef } from "react"; +import { + EmptyTrack, + SquishBigBed +} from "umms-gb"; +import { DNALogo, Y } from "logots-react" +import {MOTIFS} from "./allmotifs" +import { Typography } from "@mui/material"; +export type GenomicRange = { + chromosome?: string; + start: number; + end: number; +}; + +const MotifTooltip = (props) => { + const rc = (x) => [...x].map((xx) => [...xx].reverse()).reverse() + return ( +
+ {props.rectname.split("$")[2]} + +
+ ) + } +export const TfMotifTrack = (props) => { + + const [height, setHeight] = useState(60); + const [settingsMousedOver, setSettingsMousedOver] = useState(false); + + return( + + { + setHeight(x + 40); + props.onHeightChanged && props.onHeightChanged(40 + x); + }} + data={props.data} + transform="translate(0,40)" + tooltipContent={(rect: any) => { console.log(rect,":recg"); return }} + onClick={(x: any) => { + //return window.open(`${x}`) + return window.open(`https://factorbook.org/tf/${props.assembly==="GRCh38" ? "human" : "mouse"}/${x.rectname.split("$")[2]}/motif`, "_blank") + } + } + /> + {settingsMousedOver && ( + + )} + + setSettingsMousedOver(true)} + onMouseOut={() => setSettingsMousedOver(false)} + strokeWidth={1} + transform="translate(20,0)" + onClick={props.onSettingsClick} + /> + + TF Binding sites + + ) +} \ No newline at end of file diff --git a/screen2.0/src/app/search/gbview/zoombutton.tsx b/screen2.0/src/app/search/gbview/zoombutton.tsx new file mode 100644 index 00000000..fc0fb7f8 --- /dev/null +++ b/screen2.0/src/app/search/gbview/zoombutton.tsx @@ -0,0 +1,34 @@ +import React from 'react'; +import { + Button + } from "@mui/material" +export interface Domain { + chromosome?: string; + start: number; + end: number; +}; +export type ZoomButtonProps = { + text: string; + factor: number; + domain: Domain; + onClick: (domain: Domain) => void; +}; + +const ZoomButton = ({ text, factor, domain, onClick }) => ( + +); +export default ZoomButton; \ No newline at end of file diff --git a/screen2.0/src/app/search/page.tsx b/screen2.0/src/app/search/page.tsx index b86d6171..2ccab157 100644 --- a/screen2.0/src/app/search/page.tsx +++ b/screen2.0/src/app/search/page.tsx @@ -14,6 +14,7 @@ export default async function Search({ //Get search parameters and define defaults. const mainQueryParams: MainQueryParams = { assembly: searchParams.assembly === "GRCh38" || searchParams.assembly === "mm10" ? searchParams.assembly : "GRCh38", + gene: searchParams.gene, chromosome: searchParams.chromosome ? searchParams.chromosome : "chr11", start: searchParams.start ? Number(searchParams.start) : 5205263, end: searchParams.end ? Number(searchParams.end) : 5381894, diff --git a/screen2.0/src/app/search/types.ts b/screen2.0/src/app/search/types.ts index 1847955f..4f544623 100644 --- a/screen2.0/src/app/search/types.ts +++ b/screen2.0/src/app/search/types.ts @@ -37,6 +37,7 @@ export type MainQueryParams = { chromosome: string start: number end: number + gene?: string CellLine?: boolean PrimaryCell?: boolean Tissue?: boolean diff --git a/screen2.0/src/common/components/CcreAutocomplete.tsx b/screen2.0/src/common/components/CcreAutocomplete.tsx new file mode 100644 index 00000000..1898694c --- /dev/null +++ b/screen2.0/src/common/components/CcreAutocomplete.tsx @@ -0,0 +1,138 @@ +"use client" +import * as React from "react"; +import Box from "@mui/material/Box"; +import TextField from "@mui/material/TextField"; +import Autocomplete from "@mui/material/Autocomplete"; +import Grid from "@mui/material/Grid"; +import Typography from "@mui/material/Typography"; +import { debounce } from "@mui/material/utils"; +import { Button } from "@weng-lab/psychscreen-ui-components"; +import { useRouter } from "next/navigation" + + ///search?assembly=GRCh38&chromosome=chr11&start=5205263&end=5381894&accession=EH38E1516972 + +const CCRE_AUTOCOMPLETE_QUERY = ` +query cCREQuery($accession_prefix: [String!], $limit: Int, $assembly: String!) { + cCREQuery(accession_prefix: $accession_prefix, assembly: $assembly, limit: $limit) { + accession + coordinates { + start + end + chromosome + } + } +} +`; +export const CcreAutoComplete = (props) => { + const [value, setValue] = React.useState(null); + const [inputValue, setInputValue] = React.useState(""); + const [options, setOptions] = React.useState([]); + const [ccreAccessions, setCcreAccessions] = React.useState([]); + + const router = useRouter() + const onSearchChange = async (value: any) => { + setOptions([]); + const response = await fetch("https://factorbook.api.wenglab.org/graphql", { + method: "POST", + body: JSON.stringify({ + query: CCRE_AUTOCOMPLETE_QUERY, + variables: { + assembly: props.assembly, + accession_prefix: [value], + limit: 100 + }, + }), + headers: { "Content-Type": "application/json" }, + }); + const ccreSuggestion = (await response.json()).data?.cCREQuery; + if (ccreSuggestion && ccreSuggestion.length > 0) { + const r = ccreSuggestion.map((g: any) => g.accession); + const ccres = ccreSuggestion.map((g: any) => { + return { + chrom: g.coordinates.chromosome, + start: g.coordinates.start, + end: g.coordinates.end, + ccreaccession: g.accession, + }; + }); + setOptions(r); + setCcreAccessions(ccres); + } else if (ccreSuggestion && ccreSuggestion.length === 0) { + setOptions([]); + setCcreAccessions([]); + } + }; + + const debounceFn = React.useCallback(debounce(onSearchChange, 500), []); + + return ( + + + { + if (event.key === "Enter") { + event.defaultPrevented = true; + + if (value) { + let chrom = ccreAccessions.find((g) => g.ccreaccession === value)?.chrom + let start = ccreAccessions.find((g) => g.ccreaccession === value)?.start + let end = ccreAccessions.find((g) => g.ccreaccession === value)?.end + router.push(`search?assembly=${props.assembly}&chromosome=${chrom}&start=${start}&end=${end}&accession=${value}`) + + } + } + }} + value={value} + onChange={(_: any, newValue: string | null) => { + setValue(newValue); + }} + + inputValue={inputValue} + onInputChange={(event, newInputValue) => { + if (newInputValue != "") { + debounceFn(newInputValue); + } + + setInputValue(newInputValue); + }} + noOptionsText="e.g. EH38E0001314" + renderInput={(params) => ( + + )} + renderOption={(props, option) => { + return ( +
  • + + + + {option} + + {ccreAccessions && ccreAccessions.find((g) => g.ccreaccession === option) && ( + + {`${ccreAccessions.find((g) => g.ccreaccession === option)?.chrom}:${ + ccreAccessions.find((g) => g.ccreaccession === option)?.start + }:${ccreAccessions.find((g) => g.ccreaccession === option)?.end}`} + + )} + + +
    • + ); + }} + /> +     + +     + ); +}; diff --git a/screen2.0/src/common/components/CelltypeAutocomplete.tsx b/screen2.0/src/common/components/CelltypeAutocomplete.tsx new file mode 100644 index 00000000..f94bdda8 --- /dev/null +++ b/screen2.0/src/common/components/CelltypeAutocomplete.tsx @@ -0,0 +1,117 @@ +import React, { useMemo, useState, useRef, useCallback, useEffect } from "react"; +import Box from "@mui/material/Box"; +import TextField from "@mui/material/TextField"; +import Autocomplete from "@mui/material/Autocomplete"; +import Grid from "@mui/material/Grid"; +import Typography from "@mui/material/Typography"; +import { debounce } from "@mui/material/utils"; +import { useRouter } from "next/navigation" +import { gql, useQuery } from "@apollo/client"; + +export const CelltypeAutocomplete = (props) => { + const [value, setValue] = useState(null); + const [inputValue, setInputValue] = useState(""); + const [options, setOptions] = useState([]); + const [cellTypes, setCelltypes] = useState([]); + const [loading, setLoading] = useState(false) + const router = useRouter() + + useEffect(() => { + fetch("https://downloads.wenglab.org/databyct.json") + .then((response) => { + + return response.json() + }) + .then((data) => { + //setCellTypes(data) + let byCt = Object.keys(data.byCellType).map(ct=>{ + return { + value: ct, + tissue: data.byCellType[ct][0].tissue, + biosample_summary: data.byCellType[ct][0].biosample_summary+":chr11:5205263-5381894", + } + }) + setOptions(byCt.map(ct=>ct.biosample_summary)) + setCelltypes(byCt) + setLoading(false) + }) + .catch((error: Error) => { + // logging + // throw error + }) + setLoading(true) + }, [props.assembly]) + + + + return ( + + + { + if (event.key === "Enter") { + event.defaultPrevented = true; + + if (value) { + + let tissue = cellTypes.find((g) => g.biosample_summary === value)?.tissue + let biosample = cellTypes.find((g) => g.biosample_summary === value)?.value + let biosample_summary = value.split(":")[0] + let chromosome = value.split(":")[1] + let start = value.split(":")[2].split("-")[0] + let end = value.split(":")[2].split("-")[1] + router.push(`search?assembly=${props.assembly}&chromosome=${chromosome}&start=${Math.max(0,start)}&end=${end}&BiosampleTissue=${tissue}&BiosampleSummary=${biosample_summary}&Biosample=${biosample}`) + } + } + }} + value={value} + onChange={(_: any, newValue: string | null) => { + setValue(newValue); + }} + inputValue={inputValue} + onInputChange={(event, newInputValue) => { + if (newInputValue != "") { + //debounceFn(newInputValue); + } + + setInputValue(newInputValue); + }} + noOptionsText="e.g. LNCAP" + renderInput={(params) => ( + + )} + renderOption={(props, option) => { + return ( +
  • + + + + {option} + + {cellTypes && cellTypes.find((g) => g.biosample_summary === option) && ( + + {`${cellTypes.find((g) => g.biosample_summary === option)?.tissue}`} + + )} + + +
    • + ); + }} + /> +     + +     + ); +}; diff --git a/screen2.0/src/common/components/GeneAutocomplete.tsx b/screen2.0/src/common/components/GeneAutocomplete.tsx new file mode 100644 index 00000000..91a22f00 --- /dev/null +++ b/screen2.0/src/common/components/GeneAutocomplete.tsx @@ -0,0 +1,198 @@ +import * as React from "react"; +import Box from "@mui/material/Box"; +import TextField from "@mui/material/TextField"; +import Autocomplete from "@mui/material/Autocomplete"; +import Grid from "@mui/material/Grid"; +import Typography from "@mui/material/Typography"; +import { debounce } from "@mui/material/utils"; +import { useRouter } from "next/navigation" + +export type QueryResponse = [ + number, + string[], + any, + [string, string, string, string, string, string][], + string[] + ]; + +const GENE_AUTOCOMPLETE_QUERY = ` +query ($assembly: String!, $name_prefix: [String!], $limit: Int) { + gene(assembly: $assembly, name_prefix: $name_prefix, limit: $limit) { + name + id + coordinates { + start + chromosome + end + } + } + } + `; + +export const GeneAutoComplete = (props) => { + const [value, setValue] = React.useState(null); + const [inputValue, setInputValue] = React.useState(""); + const [options, setOptions] = React.useState([]); + const [geneids, setGeneIds] = React.useState< + { chrom: string; start: number; end: number; id: string; name: string }[] + >([]); + + const router = useRouter() + const [geneDesc, setgeneDesc] = + React.useState<{ name: string; desc: string }[]>(); + + React.useEffect(() => { + const fetchData = async () => { + let f = await Promise.all( + options.map((gene) => + fetch( + "https://clinicaltables.nlm.nih.gov/api/ncbi_genes/v3/search?authenticity_token=&terms=" + + gene.toUpperCase() + ) + .then((x) => x && x.json()) + .then((x) => { + const matches = + (x as QueryResponse)[3] && + (x as QueryResponse)[3].filter( + (x) => x[3] === gene.toUpperCase() + ); + return { + desc: + matches && matches.length >= 1 + ? matches[0][4] + : "(no description available)", + name: gene, + }; + }) + .catch(() => { + return { desc: "(no description available)", name: gene }; + }) + ) + ); + setgeneDesc(f); + }; + + options && fetchData(); + }, [options]); + + const onSearchChange = async (value: string) => { + setOptions([]); + const response = await fetch("https://ga.staging.wenglab.org/graphql", { + method: "POST", + body: JSON.stringify({ + query: GENE_AUTOCOMPLETE_QUERY, + variables: { + assembly: "GRCh38", + name_prefix: value, + limit: 1000, + }, + }), + headers: { "Content-Type": "application/json" }, + }); + const genesSuggestion = (await response.json()).data?.gene; + if (genesSuggestion && genesSuggestion.length > 0) { + const r = genesSuggestion.map((g) => g.name); + const g = genesSuggestion.map((g) => { + return { + chrom: g.coordinates.chromosome, + start: g.coordinates.start, + end: g.coordinates.end, + id: g.id, + name: g.name, + }; + }); + setOptions(r); + setGeneIds(g); + } else if (genesSuggestion && genesSuggestion.length === 0) { + setOptions([]); + setGeneIds([]); + } + }; + + const debounceFn = React.useCallback(debounce(onSearchChange, 500), []); + const gridsize = props.gridsize || 5.5; + return ( + + {props.showTitle && ( + + Search gene: +
    +     + )} + + { + if (event.key === "Enter") { + event.defaultPrevented = true; + console.log("value",value) + value && + props.onSelected && + props.onSelected({ + geneid: geneids + .find((g) => g.name === value) + ?.id.split(".")[0], + chromosome: geneids.find((g) => g.name === value)?.chrom, + start: geneids.find((g) => g.name === value)?.start, + end: geneids.find((g) => g.name === value)?.end, + }); + if (value) + { + let chrom = geneids.find((g) => g.name === value)?.chrom + let start = geneids.find((g) => g.name === value)?.start + let end = geneids.find((g) => g.name === value)?.end + router.push(`search?assembly=${props.assembly}&chromosome=${chrom}&start=${start}&end=${end}&gene=${value}`) + + } + + } + }} + value={value} + onChange={(_: any, newValue: string | null) => { + setValue(newValue); + }} + inputValue={inputValue} + onInputChange={(event, newInputValue) => { + if (newInputValue != "") { + debounceFn(newInputValue); + } + + setInputValue(newInputValue); + }} + noOptionsText="e.g sox4,gapdh" + renderInput={(params) => ( + + )} + renderOption={(props, option) => { + return ( +
  • + + + + {option} + + {geneDesc && geneDesc.find((g) => g.name === option) && ( + + {geneDesc.find((g) => g.name === option)?.desc} + + )} + + +
    • + ); + }} + /> +     +     + ); +}; diff --git a/screen2.0/src/common/components/MainSearch.tsx b/screen2.0/src/common/components/MainSearch.tsx index fccf80a4..89b8c0c9 100644 --- a/screen2.0/src/common/components/MainSearch.tsx +++ b/screen2.0/src/common/components/MainSearch.tsx @@ -1,23 +1,31 @@ "use client" -import * as React from "react" - +import React, {useState} from "react" +import Grid from "@mui/material/Grid"; import { InputBase, Switch, Stack, Typography, TextField, FormHelperText, IconButton, InputAdornment, InputBaseProps } from "@mui/material" - import SearchIcon from "@mui/icons-material/Search" - import GenomeSwitch from "./GenomeSwitch" - import { useRouter } from "next/navigation" - +import MenuItem from "@mui/material/MenuItem"; +import FormControl from "@mui/material/FormControl"; +import Select, { SelectChangeEvent } from "@mui/material/Select"; +import { CcreAutoComplete } from "./CcreAutocomplete"; +import { GeneAutoComplete } from "./GeneAutocomplete"; +import { SnpAutoComplete} from "./SnpAutocomplete"; +import { CelltypeAutocomplete } from "./CelltypeAutocomplete" export type MainSearchProps = InputBaseProps & { //false for human, true for mouse initialChecked?: boolean } const MainSearch: React.FC = (props: MainSearchProps) => { - const [value, setValue] = React.useState("") - const [checked, setChecked] = React.useState(props.initialChecked || false) - + const [value, setValue] = useState("") + const [checked, setChecked] = useState(props.initialChecked || false) + const [selectedSearch, setSelectedSearch] = useState("Genomic Region"); + const assembly = checked ? "mm10" : "GRCh38" + const handleSearchChange = (event: SelectChangeEvent) => { + + setSelectedSearch(event.target.value); + }; const router = useRouter() const handleChange = (event: { target: { value: React.SetStateAction } }) => { @@ -41,12 +49,30 @@ const MainSearch: React.FC = (props: MainSearchProps) => { return ( - + + + + + + + {selectedSearch==="Genomic Region" ? = (props: MainSearchProps) => { ), }} - sx={{ mr: "1em" }} - /> + sx={{ mr: "1em", ml:"1em" }} + /> : selectedSearch==="Gene Name" ? : selectedSearch==="SNP rsID" ? : selectedSearch==="Cell Type"? : } + + setChecked(checked)} /> + +     ) } diff --git a/screen2.0/src/common/components/SnpAutocomplete.tsx b/screen2.0/src/common/components/SnpAutocomplete.tsx new file mode 100644 index 00000000..bbb47ded --- /dev/null +++ b/screen2.0/src/common/components/SnpAutocomplete.tsx @@ -0,0 +1,133 @@ +import * as React from "react"; +import Box from "@mui/material/Box"; +import TextField from "@mui/material/TextField"; +import Autocomplete from "@mui/material/Autocomplete"; +import Grid from "@mui/material/Grid"; +import Typography from "@mui/material/Typography"; +import { debounce } from "@mui/material/utils"; +import { useRouter } from "next/navigation" + +const SNP_AUTOCOMPLETE_QUERY = ` +query snpAutocompleteQuery($snpid: String!, $assembly: String!) { + snpAutocompleteQuery(snpid: $snpid, assembly: $assembly) { + id + coordinates { + chromosome + start + end + } + } +} +`; +export const SnpAutoComplete = (props) => { + const [value, setValue] = React.useState(null); + const [inputValue, setInputValue] = React.useState(""); + const [options, setOptions] = React.useState([]); + const [snpids, setSnpIds] = React.useState([]); + const router = useRouter() + + const onSearchChange = async (value: any) => { + setOptions([]); + const response = await fetch("https://ga.staging.wenglab.org/graphql", { + method: "POST", + body: JSON.stringify({ + query: SNP_AUTOCOMPLETE_QUERY, + variables: { + assembly: "grch38", + snpid: value, + }, + }), + headers: { "Content-Type": "application/json" }, + }); + const snpSuggestion = (await response.json()).data?.snpAutocompleteQuery; + if (snpSuggestion && snpSuggestion.length > 0) { + const r = snpSuggestion.map((g: any) => g.id); + const snp = snpSuggestion.map((g: any) => { + return { + chrom: g.coordinates.chromosome, + start: g.coordinates.start, + end: g.coordinates.end, + id: g.id, + }; + }); + setOptions(r); + setSnpIds(snp); + } else if (snpSuggestion && snpSuggestion.length === 0) { + setOptions([]); + setSnpIds([]); + } + //setgeneCards([]); + }; + + const debounceFn = React.useCallback(debounce(onSearchChange, 500), []); + + return ( + + + { + if (event.key === "Enter") { + event.defaultPrevented = true; + + if (value) { + + let chromosome = snpids.find((g) => g.id === value)?.chrom + let start= snpids.find((g) => g.id === value)?.start - 2000 + let end= snpids.find((g) => g.id === value)?.end + 2000 + router.push(`search?assembly=${props.assembly}&chromosome=${chromosome}&start=${Math.max(0,start)}&end=${end}&snpid=${value}`) + } + } + }} + value={value} + onChange={(_: any, newValue: string | null) => { + setValue(newValue); + }} + inputValue={inputValue} + onInputChange={(event, newInputValue) => { + if (newInputValue != "") { + debounceFn(newInputValue); + } + + setInputValue(newInputValue); + }} + noOptionsText="e.g. rs11669173" + renderInput={(params) => ( + + )} + renderOption={(props, option) => { + return ( +
  • + + + + {option} + + {snpids && snpids.find((g) => g.id === option) && ( + + {`${snpids.find((g) => g.id === option)?.chrom}:${ + snpids.find((g) => g.id === option)?.start + }:${snpids.find((g) => g.id === option)?.end}`} + + )} + + +
    • + ); + }} + /> +     + +     + ); +}; diff --git a/screen2.0/yarn.lock b/screen2.0/yarn.lock index d0cafcae..867784be 100644 --- a/screen2.0/yarn.lock +++ b/screen2.0/yarn.lock @@ -1,8008 +1,5330 @@ -# This file is generated by running "yarn install" inside your project. -# Manual changes might be lost - proceed with caution! - -__metadata: - version: 6 - cacheKey: 8 - -"@aashutoshrathi/word-wrap@npm:^1.2.3": - version: 1.2.6 - resolution: "@aashutoshrathi/word-wrap@npm:1.2.6" - checksum: ada901b9e7c680d190f1d012c84217ce0063d8f5c5a7725bb91ec3c5ed99bb7572680eb2d2938a531ccbaec39a95422fcd8a6b4a13110c7d98dd75402f66a0cd - languageName: node - linkType: hard - -"@alloc/quick-lru@npm:^5.2.0": - version: 5.2.0 - resolution: "@alloc/quick-lru@npm:5.2.0" - checksum: bdc35758b552bcf045733ac047fb7f9a07c4678b944c641adfbd41f798b4b91fffd0fdc0df2578d9b0afc7b4d636aa6e110ead5d6281a2adc1ab90efd7f057f8 - languageName: node - linkType: hard +# THIS IS AN AUTOGENERATED FILE. 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.../src/app/search/gbview/ccretooltip.tsx | 190 +- screen2.0/src/app/search/gbview/controls.tsx | 77 +- .../src/app/search/gbview/cytobandview.tsx | 176 +- .../src/app/search/gbview/defaulttracks.tsx | 583 +- .../src/app/search/gbview/egenetracks.tsx | 179 +- .../app/search/gbview/genomebrowserview.tsx | 480 +- .../src/app/search/gbview/shiftbutton.tsx | 61 +- .../src/app/search/gbview/tfmotiftrack.tsx | 167 +- .../src/app/search/gbview/zoombutton.tsx | 65 +- .../common/components/MainResultsTable.tsx | 22 +- .../src/common/components/MainSearch.tsx | 108 - .../common/components/ResponsiveAppBar.tsx | 36 +- .../{ => mainsearch}/CcreAutocomplete.tsx | 292 +- .../{ => mainsearch}/CelltypeAutocomplete.tsx | 253 +- .../{ => mainsearch}/GeneAutocomplete.tsx | 392 +- .../components/mainsearch/MainSearch.tsx | 123 + .../{ => mainsearch}/SnpAutocomplete.tsx | 285 +- screen2.0/yarn.lock | 138 +- 32 files changed, 7701 insertions(+), 7758 deletions(-) delete mode 100644 screen2.0/src/common/components/MainSearch.tsx rename screen2.0/src/common/components/{ => mainsearch}/CcreAutocomplete.tsx (60%) rename screen2.0/src/common/components/{ => mainsearch}/CelltypeAutocomplete.tsx (52%) rename screen2.0/src/common/components/{ => mainsearch}/GeneAutocomplete.tsx (55%) create mode 100644 screen2.0/src/common/components/mainsearch/MainSearch.tsx rename screen2.0/src/common/components/{ => mainsearch}/SnpAutocomplete.tsx (52%) diff --git a/screen2.0/package.json b/screen2.0/package.json index 8616a867..205c75d7 100644 --- a/screen2.0/package.json +++ b/screen2.0/package.json @@ -41,6 +41,7 @@ "@emotion/styled": "^11.11.0", "@mui/icons-material": "^5.14.3", "@mui/material": "^5.14.2", + "@mui/styles": "^5.14.5", "@types/node": "^20.4.9", "@types/react": "^18.2.19", "@types/react-dom": "18.2.7", diff --git a/screen2.0/src/app/applets/differential-gene-expression/options.tsx b/screen2.0/src/app/applets/differential-gene-expression/options.tsx index c37e5d6c..49f03d8a 100644 --- a/screen2.0/src/app/applets/differential-gene-expression/options.tsx +++ b/screen2.0/src/app/applets/differential-gene-expression/options.tsx @@ -30,63 +30,63 @@ export function CoordinateRangeField(props: { console.log(value) if (value[0].split(",").length > 0) { let j: string = "" - for (let c of value[0].split(",")){ + for (let c of value[0].split(",")) { j += c } value[0] = j - } + } if (value[1].split(",").length > 0) { let j: string = "" - for (let c of value[1].split(",")){ + for (let c of value[1].split(",")) { j += c } value[1] = j - } + } console.log(value) if (parseInt(value[1]) - parseInt(value[0]) <= 500000 && parseInt(value[1]) - parseInt(value[0]) > 0) props.setdr([parseInt(value[0]), parseInt(value[1])]) - // variant === "min" - // ? props.setdr([parseInt(value[0]), props.dr[1]]) - // : props.setdr([props.dr[0], parseInt(value[1])]) + // variant === "min" + // ? props.setdr([parseInt(value[0]), props.dr[1]]) + // : props.setdr([props.dr[0], parseInt(value[1])]) }} onKeyDown={(e) => { if (e.key === "Enter") { - if (props.range.x.end - props.dr[0] > 0 && props.range.x.end - props.dr[0] <= 500000) { - props.setRange({ - x: { - start: props.dr[0], - end: props.range.x.end, - }, - y: { - start: props.range.y.start, - end: props.range.y.end, - }, - }) - props.setSlider({ - x1: props.dr[0], - x2: props.range.x.end, - min: props.dr[0], - max: props.range.x.end, - }) - } else return - if (props.dr[1] - props.range.x.start > 0 && props.dr[1] - props.range.x.start <= 500000) { - props.setRange({ - x: { - start: props.range.x.start, - end: props.dr[1], - }, - y: { - start: props.range.y.start, - end: props.range.y.end, - }, - }) - props.setSlider({ - x1: props.range.x.start, - x2: props.dr[1], - min: props.range.x.start, - max: props.dr[1], - }) - } else return + if (props.range.x.end - props.dr[0] > 0 && props.range.x.end - props.dr[0] <= 500000) { + props.setRange({ + x: { + start: props.dr[0], + end: props.range.x.end, + }, + y: { + start: props.range.y.start, + end: props.range.y.end, + }, + }) + props.setSlider({ + x1: props.dr[0], + x2: props.range.x.end, + min: props.dr[0], + max: props.range.x.end, + }) + } else return + if (props.dr[1] - props.range.x.start > 0 && props.dr[1] - props.range.x.start <= 500000) { + props.setRange({ + x: { + start: props.range.x.start, + end: props.dr[1], + }, + y: { + start: props.range.y.start, + end: props.range.y.end, + }, + }) + props.setSlider({ + x1: props.range.x.start, + x2: props.dr[1], + min: props.range.x.start, + max: props.dr[1], + }) + } else return } }} /> @@ -119,7 +119,9 @@ export function CoordinateRangeField(props: { }) } else return }} - >Set + > + Set + ) } diff --git a/screen2.0/src/app/applets/differential-gene-expression/page.tsx b/screen2.0/src/app/applets/differential-gene-expression/page.tsx index 9892c74b..45f05303 100644 --- a/screen2.0/src/app/applets/differential-gene-expression/page.tsx +++ b/screen2.0/src/app/applets/differential-gene-expression/page.tsx @@ -13,7 +13,20 @@ import ArrowBackIosIcon from "@mui/icons-material/ArrowBackIos" import ExpandMoreIcon from "@mui/icons-material/ExpandMore" import { ThemeProvider } from "@mui/material/styles" import { defaultTheme } from "../../../common/lib/themes" -import { Box, FormGroup, Slider, Typography, IconButton, Paper, Chip, Drawer, AppBar, AccordionSummary, AccordionDetails, Accordion } from "@mui/material" +import { + Box, + FormGroup, + Slider, + Typography, + IconButton, + Paper, + Chip, + Drawer, + AppBar, + AccordionSummary, + AccordionDetails, + Accordion, +} from "@mui/material" import { useQuery } from "@apollo/client" import { GENE_SEARCH_QUERY, ZSCORE_QUERY } from "./queries" @@ -402,141 +415,149 @@ export default function DifferentialGeneExpression() { Cell Type 1 - row.biosample_summary }, - { header: "Experiment", value: (row: any) => row.expID, render: (row: any) => createLink("https://encodeproject.org/experiments/", row.expID)}, - { header: "Tissue", value: (row: any) => row.tissue }, - ]} - onRowClick={(row: any) => { - setct1(row.value) - setTitle({ - ct1: { - name: row.name, - expID: row.expID, - }, - ct2: title.ct2, - }) - if (rowHighlight) setRowHighlight([row, rowHighlight[1]]) - else setRowHighlight([row]) - }} - sortDescending={true} - searchable={true} - dense={true} - /> + row.biosample_summary }, + { + header: "Experiment", + value: (row: any) => row.expID, + render: (row: any) => createLink("https://encodeproject.org/experiments/", row.expID), + }, + { header: "Tissue", value: (row: any) => row.tissue }, + ]} + onRowClick={(row: any) => { + setct1(row.value) + setTitle({ + ct1: { + name: row.name, + expID: row.expID, + }, + ct2: title.ct2, + }) + if (rowHighlight) setRowHighlight([row, rowHighlight[1]]) + else setRowHighlight([row]) + }} + sortDescending={true} + searchable={true} + dense={true} + /> - }> + }> Cell Type 2 row.biosample_summary }, - { header: "Experiment", value: (row: any) => row.expID, render: (row: any) => createLink("https://encodeproject.org/experiments/", row.expID)}, - { header: "Tissue", value: (row: any) => row.tissue }, - ]} - onRowClick={(row: any) => { - setct2(row.value) - setTitle({ - ct1: title.ct1, - ct2: { - name: row.name, - expID: row.expID, - }, - }) - if (rowHighlight) setRowHighlight([rowHighlight[0], row]) - else setRowHighlight([row]) - }} - sortDescending={true} - searchable={true} - dense={true} - /> + highlighted={rowHighlight ? rowHighlight[1] : false} + page={1} + rows={cellTypes["cellTypeInfoArr"]} + columns={[ + { header: "Cell Type", value: (row: any) => row.biosample_summary }, + { + header: "Experiment", + value: (row: any) => row.expID, + render: (row: any) => createLink("https://encodeproject.org/experiments/", row.expID), + }, + { header: "Tissue", value: (row: any) => row.tissue }, + ]} + onRowClick={(row: any) => { + setct2(row.value) + setTitle({ + ct1: title.ct1, + ct2: { + name: row.name, + expID: row.expID, + }, + }) + if (rowHighlight) setRowHighlight([rowHighlight[0], row]) + else setRowHighlight([row]) + }} + sortDescending={true} + searchable={true} + dense={true} + /> - Filters - - - - - - - - - - - - - - Coordinate Range: - { - if (value[0] > value[1]) return <> - if (value[0] !== slider.x1) { - setSlider({ - x1: value[0], - x2: slider.x2, - min: slider.min, - max: slider.max, - }) - setdr([value[0], dr[1]]) - setRange({ - x: { - start: value[0], - end: range.x.end, - }, - y: { - start: range.y.start, - end: range.y.end, - }, - }) - } else { - setSlider({ - x1: slider.x1, - x2: value[1], - min: slider.min, - max: slider.max, - }) - setdr([dr[0], value[1]]) - setRange({ - x: { - start: range.x.start, - end: value[1], - }, - y: { - start: range.y.start, - end: range.y.end, - }, - }) - } - }} - /> - - - + Filters + + + + + + + + + + + + + + Coordinate Range: + { + if (value[0] > value[1]) return <> + if (value[0] !== slider.x1) { + setSlider({ + x1: value[0], + x2: slider.x2, + min: slider.min, + max: slider.max, + }) + setdr([value[0], dr[1]]) + setRange({ + x: { + start: value[0], + end: range.x.end, + }, + y: { + start: range.y.start, + end: range.y.end, + }, + }) + } else { + setSlider({ + x1: slider.x1, + x2: value[1], + min: slider.min, + max: slider.max, + }) + setdr([dr[0], value[1]]) + setRange({ + x: { + start: range.x.start, + end: value[1], + }, + y: { + start: range.y.start, + end: range.y.end, + }, + }) + } + }} + /> + + + ) diff --git a/screen2.0/src/app/applets/differential-gene-expression/plot.tsx b/screen2.0/src/app/applets/differential-gene-expression/plot.tsx index f8615f4f..67024908 100644 --- a/screen2.0/src/app/applets/differential-gene-expression/plot.tsx +++ b/screen2.0/src/app/applets/differential-gene-expression/plot.tsx @@ -73,9 +73,7 @@ export function PlotDifferentialExpression(props: { <> ) : ( - - log2 gene expression fold change - + log2 gene expression fold change )} {!props.toggleccres ? ( diff --git a/screen2.0/src/app/applets/differential-gene-expression/queries.ts b/screen2.0/src/app/applets/differential-gene-expression/queries.ts index 1076cd2a..22dd0be1 100644 --- a/screen2.0/src/app/applets/differential-gene-expression/queries.ts +++ b/screen2.0/src/app/applets/differential-gene-expression/queries.ts @@ -70,4 +70,4 @@ export const ZSCORE_QUERY = gql` } } } -` \ No newline at end of file +` diff --git a/screen2.0/src/app/applets/differential-gene-expression/utils.tsx b/screen2.0/src/app/applets/differential-gene-expression/utils.tsx index 1c91789d..e2c81037 100644 --- a/screen2.0/src/app/applets/differential-gene-expression/utils.tsx +++ b/screen2.0/src/app/applets/differential-gene-expression/utils.tsx @@ -268,8 +268,8 @@ export const GenePoint = (props: { point: Gene; i: number; range: Range2D; dimen console.log(tmp) // transform - p1 = linearTransform2D(props.range, props.dimensions)({ x: x1, y: (props.i+props.range.y.start)*tmp }) - p2 = linearTransform2D(props.range, props.dimensions)({ x: x2, y: (props.i+props.range.y.start)*tmp }) + p1 = linearTransform2D(props.range, props.dimensions)({ x: x1, y: (props.i + props.range.y.start) * tmp }) + p2 = linearTransform2D(props.range, props.dimensions)({ x: x2, y: (props.i + props.range.y.start) * tmp }) // tooltip for mouseover const GeneTooltip = () => { @@ -423,9 +423,7 @@ export const SetRange_y = (props: { let r: number = range_y[range_y.length - 1] // last label in list let cellTypeLabel: string[] = [ "translate(39," + t.y.toString() + ") rotate(-90)", - "translate(39," + - (t.y + (props.title.ct1.expID.length === 0 ? 32.5 : 32.5)).toString() + - ") rotate(-90)", + "translate(39," + (t.y + (props.title.ct1.expID.length === 0 ? 32.5 : 32.5)).toString() + ") rotate(-90)", ] // console.log(props.title.ct1.name.length) // console.log(document.getElementById(props.title.ct1.name).clientWidth) @@ -435,11 +433,11 @@ export const SetRange_y = (props: { const getName = (name: string) => { let cellname: string = "" - for (let c of name){ + for (let c of name) { if (c === "(") break else cellname += c } - return cellname += " " + return (cellname += " ") } if (y === 0.0) @@ -456,7 +454,7 @@ export const SetRange_y = (props: { - + ◄ {getName(props.title.ct1.name)} diff --git a/screen2.0/src/app/applets/gene-expression/const.ts b/screen2.0/src/app/applets/gene-expression/const.ts index 8201fc4c..c5b9bae7 100644 --- a/screen2.0/src/app/applets/gene-expression/const.ts +++ b/screen2.0/src/app/applets/gene-expression/const.ts @@ -1 +1,2 @@ -export const GeneExpressionInfoTooltip = "This bar plot displays the expression level of a given gene across available cell types and tissues derived from RNA-seq data. By default, the data displayed is log2(TPM + 0.01), but this may be customized by selecting from the data dropdown; FPKM values are also available and the log scale may be turned off. TPM and RPKM are two metrics of gene expression levels and they differ slightly in their approaches to normalizing for sequencing depth and gene length. The sort order dropdown allows sorting of the data by TPM or FPKM and also allows grouping of the expression values by tissue. Mousing over the bars displays more information about the expriments that produced the data points, and clicking on a bar redirects to the corresponging experiment at the ENCODE portal." \ No newline at end of file +export const GeneExpressionInfoTooltip = + "This bar plot displays the expression level of a given gene across available cell types and tissues derived from RNA-seq data. By default, the data displayed is log2(TPM + 0.01), but this may be customized by selecting from the data dropdown; FPKM values are also available and the log scale may be turned off. TPM and RPKM are two metrics of gene expression levels and they differ slightly in their approaches to normalizing for sequencing depth and gene length. The sort order dropdown allows sorting of the data by TPM or FPKM and also allows grouping of the expression values by tissue. Mousing over the bars displays more information about the expriments that produced the data points, and clicking on a bar redirects to the corresponging experiment at the ENCODE portal." diff --git a/screen2.0/src/app/applets/gene-expression/page.tsx b/screen2.0/src/app/applets/gene-expression/page.tsx index a916b48a..deba0022 100644 --- a/screen2.0/src/app/applets/gene-expression/page.tsx +++ b/screen2.0/src/app/applets/gene-expression/page.tsx @@ -16,7 +16,7 @@ import { ThemeProvider } from "@mui/material/styles" import { defaultTheme } from "../../../common/lib/themes" import MenuIcon from "@mui/icons-material/Menu" import ArrowBackIosIcon from "@mui/icons-material/ArrowBackIos" -import InfoIcon from '@mui/icons-material/Info'; +import InfoIcon from "@mui/icons-material/Info" import Image from "next/image" import GeneAutoComplete from "./gene-autocomplete" diff --git a/screen2.0/src/app/applets/gene-expression/utils.tsx b/screen2.0/src/app/applets/gene-expression/utils.tsx index 337f99bf..68c2e8fa 100644 --- a/screen2.0/src/app/applets/gene-expression/utils.tsx +++ b/screen2.0/src/app/applets/gene-expression/utils.tsx @@ -26,7 +26,7 @@ export function PlotGeneExpression(props: { }) { const router = useRouter() const [collapse, setCollapse] = useState<{ [id: string]: boolean }>({}) - const[highlighted, setHighlighted] = useState("") + const [highlighted, setHighlighted] = useState("") let itemsRID: RIDItemList = props.data[props.RNAtype]["itemsByRID"] let tissues: { [id: string]: { sum: number; values: GeneExpEntry[] } } = {} // dict of ftissues @@ -64,19 +64,26 @@ export function PlotGeneExpression(props: { p1 = linearTransform2D(props.range, props.dimensions)({ x: item.value, y: 0 }) return ( - router.push("https://encodeproject.org/experiments/" + item.expID)} - onMouseEnter={() => { - setHighlighted(item.expID) - }} - onMouseOut={() => { - setHighlighted("") - }} - onMouseOver={() => { - setHighlighted(item.expID) - }}> + router.push("https://encodeproject.org/experiments/" + item.expID)} + onMouseEnter={() => { + setHighlighted(item.expID) + }} + onMouseOut={() => { + setHighlighted("") + }} + onMouseOver={() => { + setHighlighted(item.expID) + }} + > {item.cellType + "\n" + item.value} - {highlighted === item.expID ? : <>} + {highlighted === item.expID ? : <>} {Number(item.value.toFixed(3)) + " "} {item.expID} diff --git a/screen2.0/src/app/page.tsx b/screen2.0/src/app/page.tsx index ddbd87ee..0860da6b 100644 --- a/screen2.0/src/app/page.tsx +++ b/screen2.0/src/app/page.tsx @@ -3,7 +3,7 @@ "use client" import { Typography } from "@mui/material" -import MainSearch from "../common/components/MainSearch" +import MainSearch from "../common/components/mainsearch/MainSearch" // Grid v2 isn't declared stable yet, but using it now as it's what MUI is currently developing out import Grid2 from "@mui/material/Unstable_Grid2/Grid2" diff --git a/screen2.0/src/app/search/ccredetails/const.ts b/screen2.0/src/app/search/ccredetails/const.ts index eefb8706..c12d07cb 100644 --- a/screen2.0/src/app/search/ccredetails/const.ts +++ b/screen2.0/src/app/search/ccredetails/const.ts @@ -1 +1,2 @@ -export const RampageToolTipInfo = "RAMPAGE (RNA Annotiation and Mapping of Promoters for Analysis of Gene Expression) data allows for the annotation of and expression at transcription start sites with nucleotide precision. Here, we display the sum of signal (from ENCODE Data Coordination Center's RAMPAGE pipeline) in a +-50bp window around GENCODE V19 annotated TSSs for the cRE's nearest protein coding gene. As, this signal is strand specific, we display signal from both the + and - strands for each experiment." +export const RampageToolTipInfo = + "RAMPAGE (RNA Annotiation and Mapping of Promoters for Analysis of Gene Expression) data allows for the annotation of and expression at transcription start sites with nucleotide precision. Here, we display the sum of signal (from ENCODE Data Coordination Center's RAMPAGE pipeline) in a +-50bp window around GENCODE V19 annotated TSSs for the cRE's nearest protein coding gene. As, this signal is strand specific, we display signal from both the + and - strands for each experiment." diff --git a/screen2.0/src/app/search/ccresearch.tsx b/screen2.0/src/app/search/ccresearch.tsx index e5a04729..fd9a861b 100644 --- a/screen2.0/src/app/search/ccresearch.tsx +++ b/screen2.0/src/app/search/ccresearch.tsx @@ -37,7 +37,6 @@ export const CcreSearch = ({ mainQueryParams, ccrerows, globals, assembly }) => - {searchParams.get("accession") && } @@ -49,18 +48,27 @@ export const CcreSearch = ({ mainQueryParams, ccrerows, globals, assembly }) => - setTabIndex(val)}> + setTabIndex(val)}> - + - {tabIndex===0 && } - {tabIndex===1 && } + {tabIndex === 0 && ( + + )} + {tabIndex === 1 && ( + + )} )} diff --git a/screen2.0/src/app/search/gbview/allmotifs.ts b/screen2.0/src/app/search/gbview/allmotifs.ts index 866fc4b7..05528a6d 100644 --- a/screen2.0/src/app/search/gbview/allmotifs.ts +++ b/screen2.0/src/app/search/gbview/allmotifs.ts @@ -1,5493 +1,5492 @@ -export const MOTIFS = { - IRF1: [ - [0.323, 0.103, 0.503, 0.071], - [0.536, 0.179, 0.258, 0.028], - [0.818, 0.09, 0.058, 0.034], - [0.906, 0.0, 0.077, 0.017], - [0.182, 0.427, 0.213, 0.178], - [0.256, 0.242, 0.113, 0.39], - [0.1, 0.003, 0.898, 0.0], - [0.696, 0.3, 0.0, 0.004], - [0.837, 0.129, 0.005, 0.029], - [0.885, 0.0, 0.069, 0.046], - [0.082, 0.426, 0.46, 0.032], - [0.119, 0.292, 0.166, 0.423], - [0.422, 0.034, 0.486, 0.058], - [0.493, 0.145, 0.317, 0.045], - [0.511, 0.206, 0.151, 0.131], - [0.52, 0.098, 0.297, 0.085], - ], - HIC1: [ - [0.001, 0.022, 0.0, 0.977], - [0.06, 0.0, 0.938, 0.002], - [0.186, 0.783, 0.031, 0.0], - [0.007, 0.959, 0.002, 0.032], - [0.054, 0.934, 0.006, 0.006], - [0.261, 0.0, 0.169, 0.569], - [0.078, 0.487, 0.179, 0.255], - ], - LHX2: [ - [0.067, 0.666, 0.193, 0.074], - [0.0, 0.215, 0.0, 0.785], - [0.512, 0.446, 0.0, 0.041], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 0.003, 0.997], - [0.001, 0.018, 0.004, 0.978], - [0.988, 0.0, 0.0, 0.012], - ], - ZNF667: [ - [0.052, 0.058, 0.825, 0.064], - [0.236, 0.282, 0.331, 0.15], - [0.071, 0.083, 0.285, 0.561], - [0.074, 0.046, 0.816, 0.064], - [0.785, 0.012, 0.166, 0.037], - [0.083, 0.009, 0.902, 0.006], - [0.003, 0.936, 0.012, 0.049], - [0.028, 0.046, 0.025, 0.902], - [0.003, 0.448, 0.012, 0.537], - [0.123, 0.058, 0.12, 0.699], - [0.083, 0.028, 0.067, 0.822], - [0.758, 0.031, 0.117, 0.095], - [0.798, 0.117, 0.055, 0.031], - [0.393, 0.028, 0.518, 0.061], - [0.025, 0.043, 0.911, 0.021], - [0.077, 0.644, 0.187, 0.092], - [0.11, 0.788, 0.058, 0.043], - [0.518, 0.181, 0.086, 0.215], - [0.113, 0.712, 0.08, 0.095], - ], - ZNF341: [ - [0.008, 0.006, 0.977, 0.008], - [0.014, 0.961, 0.017, 0.009], - [0.047, 0.15, 0.053, 0.751], - [0.093, 0.309, 0.558, 0.041], - [0.027, 0.055, 0.01, 0.908], - [0.003, 0.069, 0.094, 0.834], - [0.075, 0.791, 0.088, 0.045], - [0.057, 0.685, 0.035, 0.223], - ], - TP53: [ - [0.264, 0.024, 0.526, 0.186], - [0.459, 0.0, 0.476, 0.066], - [0.017, 0.96, 0.001, 0.023], - [0.79, 0.0, 0.103, 0.106], - [0.209, 0.063, 0.019, 0.71], - [0.0, 0.004, 0.978, 0.018], - [0.055, 0.368, 0.0, 0.577], - [0.101, 0.59, 0.019, 0.289], - [0.156, 0.329, 0.136, 0.379], - [0.264, 0.177, 0.426, 0.133], - [0.251, 0.16, 0.411, 0.178], - [0.44, 0.054, 0.416, 0.09], - [0.079, 0.741, 0.153, 0.027], - [0.576, 0.225, 0.037, 0.162], - [0.269, 0.075, 0.137, 0.519], - [0.168, 0.078, 0.664, 0.09], - ], - SRF: [ - [0.258, 0.127, 0.089, 0.527], - [0.124, 0.132, 0.324, 0.419], - [0.261, 0.215, 0.293, 0.231], - [0.016, 0.968, 0.008, 0.008], - [0.0, 0.93, 0.0, 0.069], - [0.532, 0.061, 0.016, 0.39], - [0.251, 0.021, 0.017, 0.71], - [0.817, 0.009, 0.033, 0.141], - [0.131, 0.028, 0.004, 0.837], - [0.678, 0.016, 0.017, 0.29], - [0.353, 0.012, 0.061, 0.574], - [0.093, 0.0, 0.906, 0.001], - [0.032, 0.006, 0.951, 0.011], - [0.229, 0.294, 0.215, 0.262], - [0.419, 0.357, 0.109, 0.115], - [0.558, 0.077, 0.146, 0.219], - ], - SPIB: [ - [0.593, 0.068, 0.192, 0.148], - [0.602, 0.058, 0.23, 0.11], - [0.561, 0.029, 0.184, 0.227], - [0.182, 0.093, 0.697, 0.028], - [0.606, 0.102, 0.277, 0.015], - [0.088, 0.0, 0.904, 0.007], - [0.0, 0.004, 0.996, 0.0], - [0.991, 0.005, 0.001, 0.003], - [0.985, 0.0, 0.003, 0.012], - [0.052, 0.176, 0.769, 0.003], - [0.091, 0.076, 0.03, 0.803], - [0.076, 0.157, 0.738, 0.029], - ], - "NKX2-5": [ - [0.119, 0.154, 0.528, 0.2], - [0.172, 0.458, 0.144, 0.226], - [0.24, 0.026, 0.498, 0.236], - [0.247, 0.425, 0.163, 0.164], - [0.311, 0.187, 0.148, 0.353], - [0.316, 0.082, 0.427, 0.174], - [0.382, 0.249, 0.194, 0.175], - [0.147, 0.188, 0.406, 0.26], - [0.207, 0.307, 0.207, 0.279], - [0.31, 0.176, 0.316, 0.199], - [0.221, 0.319, 0.163, 0.296], - [0.087, 0.299, 0.176, 0.438], - [0.124, 0.206, 0.163, 0.507], - [0.205, 0.163, 0.216, 0.416], - [0.343, 0.07, 0.583, 0.004], - [0.987, 0.003, 0.003, 0.007], - [0.058, 0.019, 0.915, 0.007], - [0.404, 0.002, 0.021, 0.573], - [0.031, 0.002, 0.941, 0.027], - [0.055, 0.274, 0.541, 0.129], - ], - TBX5: [ - [0.195, 0.312, 0.018, 0.475], - [0.364, 0.131, 0.345, 0.16], - [0.008, 0.053, 0.099, 0.841], - [0.055, 0.745, 0.013, 0.187], - [0.615, 0.147, 0.039, 0.2], - [0.146, 0.427, 0.277, 0.149], - [0.333, 0.2, 0.078, 0.389], - [0.302, 0.273, 0.365, 0.059], - [0.547, 0.067, 0.144, 0.243], - [0.019, 0.929, 0.0, 0.052], - [0.816, 0.002, 0.081, 0.102], - [0.03, 0.834, 0.118, 0.017], - [0.168, 0.457, 0.068, 0.308], - [0.172, 0.192, 0.078, 0.558], - ], - ELK4: [ - [0.462, 0.116, 0.319, 0.103], - [0.008, 0.638, 0.097, 0.257], - [0.111, 0.0, 0.003, 0.887], - [0.002, 0.0, 0.0, 0.998], - [0.006, 0.994, 0.001, 0.0], - [0.005, 0.973, 0.0, 0.021], - [0.026, 0.021, 0.674, 0.279], - [0.053, 0.189, 0.653, 0.104], - ], - STAT3: [ - [0.082, 0.065, 0.078, 0.776], - [0.081, 0.012, 0.257, 0.649], - [0.192, 0.668, 0.07, 0.07], - [0.024, 0.748, 0.01, 0.218], - [0.313, 0.165, 0.35, 0.172], - [0.136, 0.003, 0.856, 0.005], - [0.03, 0.016, 0.819, 0.135], - [0.961, 0.028, 0.003, 0.008], - [0.964, 0.01, 0.022, 0.004], - ], - NR2F6: [ - [0.143, 0.125, 0.165, 0.567], - [0.12, 0.112, 0.629, 0.139], - [0.415, 0.123, 0.394, 0.068], - [0.484, 0.282, 0.129, 0.105], - [0.025, 0.949, 0.023, 0.003], - [0.015, 0.262, 0.028, 0.695], - [0.034, 0.196, 0.034, 0.736], - [0.007, 0.091, 0.001, 0.901], - [0.031, 0.012, 0.927, 0.03], - [0.44, 0.167, 0.271, 0.122], - [0.354, 0.392, 0.054, 0.199], - [0.05, 0.839, 0.046, 0.064], - [0.122, 0.363, 0.022, 0.493], - ], - FOXK2: [ - [0.028, 0.014, 0.014, 0.944], - [0.158, 0.004, 0.838, 0.0], - [0.003, 0.017, 0.017, 0.963], - [0.015, 0.0, 0.082, 0.903], - [0.002, 0.0, 0.126, 0.873], - [0.969, 0.007, 0.0, 0.023], - [0.0, 0.734, 0.016, 0.25], - ], - ZNF24: [ - [0.161, 0.533, 0.111, 0.195], - [0.415, 0.227, 0.193, 0.165], - [0.117, 0.311, 0.111, 0.461], - [0.172, 0.106, 0.163, 0.56], - [0.259, 0.569, 0.125, 0.047], - [0.527, 0.239, 0.131, 0.103], - [0.208, 0.089, 0.139, 0.564], - [0.056, 0.06, 0.085, 0.8], - [0.005, 0.968, 0.023, 0.004], - [0.878, 0.059, 0.037, 0.026], - [0.007, 0.149, 0.154, 0.69], - [0.059, 0.047, 0.082, 0.811], - [0.157, 0.656, 0.024, 0.163], - [0.572, 0.178, 0.178, 0.071], - [0.026, 0.091, 0.031, 0.851], - [0.036, 0.019, 0.044, 0.9], - [0.005, 0.984, 0.004, 0.007], - [0.568, 0.182, 0.149, 0.101], - ], - CEBPB: [ - [0.617, 0.049, 0.195, 0.139], - [0.0, 0.0, 0.0, 1.0], - [0.001, 0.0, 0.044, 0.955], - [0.332, 0.0, 0.286, 0.381], - [0.0, 0.998, 0.0, 0.002], - [0.65, 0.123, 0.001, 0.225], - [0.164, 0.363, 0.008, 0.466], - [0.716, 0.276, 0.0, 0.008], - [0.986, 0.001, 0.003, 0.01], - [0.021, 0.302, 0.136, 0.541], - ], - MAX: [ - [0.0, 1.0, 0.0, 0.0], - [0.96, 0.001, 0.018, 0.02], - [0.0, 0.481, 0.004, 0.515], - [0.031, 0.01, 0.96, 0.0], - [0.052, 0.154, 0.0, 0.795], - [0.0, 0.005, 0.92, 0.075], - ], - PPARG: [ - [0.098, 0.123, 0.08, 0.699], - [0.197, 0.143, 0.541, 0.119], - [0.57, 0.252, 0.129, 0.05], - [0.189, 0.72, 0.014, 0.077], - [0.05, 0.822, 0.007, 0.121], - [0.011, 0.161, 0.011, 0.816], - [0.075, 0.224, 0.037, 0.664], - [0.025, 0.061, 0.022, 0.893], - [0.132, 0.201, 0.536, 0.13], - [0.336, 0.316, 0.188, 0.159], - [0.065, 0.74, 0.043, 0.152], - [0.151, 0.727, 0.016, 0.107], - [0.063, 0.445, 0.046, 0.446], - [0.591, 0.145, 0.15, 0.114], - [0.214, 0.319, 0.335, 0.133], - [0.333, 0.09, 0.033, 0.544], - [0.196, 0.103, 0.152, 0.549], - ], - NFIA: [ - [0.057, 0.392, 0.103, 0.449], - [0.012, 0.19, 0.121, 0.677], - [0.045, 0.0, 0.847, 0.109], - [0.032, 0.063, 0.896, 0.009], - [0.286, 0.595, 0.041, 0.078], - [0.331, 0.204, 0.131, 0.334], - [0.206, 0.411, 0.171, 0.211], - [0.23, 0.209, 0.328, 0.234], - [0.187, 0.378, 0.239, 0.196], - [0.25, 0.105, 0.231, 0.413], - [0.042, 0.029, 0.746, 0.183], - [0.002, 0.93, 0.032, 0.035], - [0.0, 0.84, 0.0, 0.16], - [0.721, 0.027, 0.239, 0.013], - [0.37, 0.127, 0.454, 0.048], - ], - EPAS1: [ - [0.746, 0.021, 0.218, 0.015], - [0.002, 0.906, 0.001, 0.091], - [0.091, 0.0, 0.888, 0.021], - [0.004, 0.0, 0.004, 0.992], - [0.0, 0.0, 0.993, 0.007], - ], - JUNB: [ - [0.443, 0.231, 0.271, 0.055], - [0.0, 0.004, 0.001, 0.995], - [0.0, 0.0, 0.86, 0.14], - [0.991, 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OTX2: [ - [0.225, 0.331, 0.014, 0.43], - [0.189, 0.022, 0.002, 0.787], - [0.923, 0.005, 0.056, 0.017], - [0.991, 0.007, 0.001, 0.0], - [0.006, 0.004, 0.08, 0.91], - [0.022, 0.957, 0.015, 0.005], - [0.014, 0.762, 0.002, 0.223], - [0.118, 0.423, 0.08, 0.379], - ], - ZIC5: [ - [0.123, 0.75, 0.12, 0.006], - [0.314, 0.262, 0.215, 0.208], - [0.003, 0.981, 0.002, 0.014], - [0.503, 0.296, 0.102, 0.099], - [0.069, 0.162, 0.766, 0.003], - [0.005, 0.878, 0.005, 0.112], - [0.598, 0.002, 0.391, 0.009], - [0.005, 0.002, 0.968, 0.024], - [0.0, 0.0, 1.0, 0.0], - [0.19, 0.034, 0.674, 0.101], - [0.078, 0.045, 0.833, 0.044], - [0.04, 0.033, 0.845, 0.083], - [0.005, 0.469, 0.153, 0.373], - [0.143, 0.583, 0.221, 0.053], - ], - ZFP42: [ - [0.231, 0.1, 0.587, 0.082], - [0.154, 0.05, 0.731, 0.066], - [0.106, 0.605, 0.242, 0.048], - [0.581, 0.309, 0.082, 0.028], - [0.017, 0.017, 0.882, 0.084], - [0.099, 0.861, 0.016, 0.025], - [0.0, 1.0, 0.0, 0.0], - [0.999, 0.0, 0.001, 0.0], - [0.0, 0.0, 0.0, 1.0], - [0.058, 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0.839, 0.065, 0.094], - [0.008, 0.975, 0.007, 0.011], - [0.001, 0.991, 0.007, 0.001], - [0.85, 0.093, 0.002, 0.054], - [0.018, 0.002, 0.975, 0.005], - [0.027, 0.046, 0.81, 0.116], - [0.025, 0.864, 0.025, 0.085], - [0.036, 0.06, 0.036, 0.868], - [0.109, 0.047, 0.786, 0.059], - [0.123, 0.064, 0.757, 0.055], - [0.507, 0.069, 0.09, 0.333], - [0.077, 0.368, 0.475, 0.08], - [0.056, 0.071, 0.069, 0.804], - [0.102, 0.255, 0.463, 0.18], - [0.216, 0.469, 0.23, 0.085], - [0.801, 0.053, 0.092, 0.054], - [0.414, 0.073, 0.451, 0.062], - [0.058, 0.376, 0.078, 0.489], - [0.076, 0.082, 0.464, 0.379], - [0.091, 0.387, 0.445, 0.078], - [0.063, 0.588, 0.079, 0.27], - [0.225, 0.085, 0.283, 0.407], - [0.116, 0.3, 0.377, 0.207], - [0.269, 0.092, 0.534, 0.105], - [0.439, 0.191, 0.269, 0.1], - [0.076, 0.402, 0.071, 0.452], - [0.086, 0.451, 0.071, 0.393], - ], - NFATC2: [ - [0.535, 0.112, 0.254, 0.098], - [0.113, 0.136, 0.026, 0.725], - [0.002, 0.0, 0.998, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.998, 0.002, 0.0, 0.0], - [0.988, 0.0, 0.011, 0.0], - [0.793, 0.077, 0.021, 0.11], - [0.471, 0.238, 0.154, 0.137], - [0.443, 0.063, 0.093, 0.401], - ], - RELB: [ - [0.023, 0.035, 0.89, 0.051], - [0.004, 0.024, 0.965, 0.007], - [0.001, 0.014, 0.725, 0.261], - [0.456, 0.031, 0.459, 0.054], - [0.06, 0.506, 0.291, 0.142], - [0.007, 0.011, 0.004, 0.978], - [0.0, 0.031, 0.002, 0.967], - [0.012, 0.266, 0.015, 0.706], - [0.002, 0.868, 0.0, 0.13], - [0.051, 0.76, 0.063, 0.127], - ], - MEF2D: [ - [0.096, 0.079, 0.401, 0.424], - [0.026, 0.757, 0.101, 0.117], - [0.001, 0.026, 0.0, 0.973], - [0.974, 0.001, 0.01, 0.015], - [0.15, 0.004, 0.0, 0.846], - [0.203, 0.006, 0.006, 0.784], - [0.142, 0.048, 0.0, 0.81], - [0.276, 0.074, 0.008, 0.642], - [0.091, 0.019, 0.043, 0.848], - [0.758, 0.002, 0.237, 0.002], - [0.085, 0.033, 0.81, 0.072], - ], - ETV1: [ - [0.063, 0.764, 0.159, 0.014], - [0.512, 0.472, 0.015, 0.001], - [0.0, 0.0, 1.0, 0.0], - [0.003, 0.0, 0.997, 0.0], - [0.999, 0.0, 0.0, 0.001], - [0.827, 0.014, 0.008, 0.152], - [0.239, 0.061, 0.681, 0.018], - [0.091, 0.285, 0.141, 0.483], - ], - ZFP28: [ - [0.132, 0.048, 0.127, 0.693], - [0.067, 0.301, 0.087, 0.545], - [0.012, 0.003, 0.001, 0.984], - [0.0, 0.842, 0.0, 0.158], - [0.228, 0.205, 0.058, 0.508], - [0.615, 0.073, 0.142, 0.17], - [0.003, 0.158, 0.017, 0.822], - [0.025, 0.141, 0.013, 0.821], - [0.0, 0.019, 0.001, 0.98], - [0.0, 0.893, 0.0, 0.107], - [0.115, 0.272, 0.009, 0.605], - [0.025, 0.014, 0.023, 0.939], - [0.007, 0.693, 0.003, 0.297], - [0.188, 0.126, 0.05, 0.636], - [0.228, 0.078, 0.306, 0.389], - [0.231, 0.057, 0.464, 0.248], - [0.324, 0.051, 0.22, 0.405], - [0.191, 0.072, 0.581, 0.156], - [0.134, 0.079, 0.116, 0.671], - [0.141, 0.457, 0.204, 0.198], - [0.677, 0.069, 0.116, 0.138], - ], - ESRRA: [ - [0.518, 0.017, 0.461, 0.004], - [0.762, 0.14, 0.035, 0.062], - [0.001, 0.04, 0.959, 0.001], - [0.0, 0.0, 1.0, 0.0], - [0.039, 0.026, 0.005, 0.929], - [0.001, 0.913, 0.012, 0.075], - [0.91, 0.004, 0.086, 0.001], - ], - PAX5: [ - [0.011, 0.003, 0.86, 0.125], - [0.105, 0.162, 0.008, 0.725], - [0.0, 0.999, 0.0, 0.001], - [0.87, 0.0, 0.052, 0.079], - [0.052, 0.586, 0.029, 0.334], - [0.203, 0.016, 0.777, 0.004], - [0.003, 0.594, 0.379, 0.024], - [0.212, 0.245, 0.068, 0.475], - ], - TCF7L1: [ - [0.0, 0.928, 0.054, 0.018], - [0.003, 0.004, 0.001, 0.993], - [0.0, 0.007, 0.004, 0.989], - [0.018, 0.0, 0.01, 0.972], - [0.022, 0.102, 0.772, 0.104], - [0.898, 0.0, 0.005, 0.097], - [0.412, 0.027, 0.008, 0.552], - ], - ZBTB17: [ - [0.195, 0.22, 0.5, 0.085], - [0.182, 0.175, 0.484, 0.16], - [0.154, 0.124, 0.601, 0.121], - [0.198, 0.179, 0.163, 0.46], - [0.051, 0.107, 0.811, 0.031], - [0.026, 0.025, 0.898, 0.051], - [0.088, 0.08, 0.817, 0.015], - [0.009, 0.014, 0.921, 0.056], - [0.009, 0.009, 0.958, 0.024], - [0.431, 0.491, 0.016, 0.063], - [0.116, 0.021, 0.772, 0.091], - [0.024, 0.039, 0.899, 0.038], - [0.08, 0.033, 0.824, 0.063], - [0.04, 0.049, 0.873, 0.039], - [0.275, 0.513, 0.102, 0.11], - ], - ZNF260: [ - [0.018, 0.298, 0.034, 0.65], - [0.095, 0.785, 0.019, 0.101], - [0.052, 0.336, 0.034, 0.579], - [0.03, 0.029, 0.027, 0.914], - [0.026, 0.024, 0.033, 0.917], - [0.027, 0.026, 0.049, 0.898], - [0.187, 0.042, 0.096, 0.676], - [0.076, 0.197, 0.017, 0.711], - [0.859, 0.053, 0.042, 0.045], - [0.014, 0.18, 0.016, 0.79], - [0.154, 0.022, 0.661, 0.163], - [0.042, 0.002, 0.946, 0.009], - [0.003, 0.779, 0.019, 0.2], - [0.022, 0.032, 0.006, 0.941], - [0.028, 0.057, 0.886, 0.029], - [0.153, 0.697, 0.006, 0.144], - [0.809, 0.012, 0.175, 0.003], - [0.001, 0.004, 0.012, 0.982], - [0.918, 0.008, 0.026, 0.047], - [0.137, 0.101, 0.751, 0.011], - [0.003, 0.007, 0.014, 0.976], - [0.96, 0.005, 0.025, 0.011], - [0.002, 0.104, 0.016, 0.877], - [0.003, 0.004, 0.009, 0.984], - [0.0, 0.954, 0.003, 0.042], - [0.006, 0.945, 0.003, 0.046], - [0.861, 0.036, 0.055, 0.047], - [0.024, 0.148, 0.036, 0.792], - [0.094, 0.064, 0.53, 0.312], - [0.11, 0.068, 0.743, 0.08], - [0.067, 0.099, 0.064, 0.77], - [0.296, 0.048, 0.582, 0.075], - [0.057, 0.08, 0.056, 0.807], - [0.611, 0.049, 0.263, 0.077], - [0.149, 0.081, 0.156, 0.614], - [0.741, 0.076, 0.089, 0.095], - [0.093, 0.091, 0.073, 0.744], - [0.256, 0.049, 0.591, 0.104], - [0.091, 0.087, 0.076, 0.746], - [0.527, 0.086, 0.291, 0.096], - [0.078, 0.706, 0.06, 0.156], - [0.115, 0.702, 0.055, 0.129], - [0.731, 0.085, 0.06, 0.125], - [0.105, 0.623, 0.05, 0.222], - [0.685, 0.086, 0.084, 0.145], - [0.135, 0.094, 0.093, 0.678], - [0.097, 0.073, 0.066, 0.764], - [0.092, 0.073, 0.065, 0.77], - [0.09, 0.078, 0.066, 0.766], - [0.142, 0.545, 0.115, 0.197], - [0.093, 0.113, 0.049, 0.746], - [0.106, 0.092, 0.066, 0.736], - [0.213, 0.109, 0.052, 0.627], - [0.651, 0.084, 0.07, 0.195], - [0.123, 0.14, 0.071, 0.666], - [0.109, 0.618, 0.074, 0.2], - [0.131, 0.593, 0.076, 0.199], - [0.633, 0.108, 0.097, 0.162], - [0.173, 0.116, 0.42, 0.291], - [0.105, 0.15, 0.085, 0.66], - [0.123, 0.591, 0.079, 0.207], - [0.191, 0.18, 0.088, 0.541], - [0.47, 0.151, 0.129, 0.251], - [0.121, 0.293, 0.082, 0.505], - ], - ZNF490: [ - [0.218, 0.128, 0.143, 0.511], - [0.214, 0.123, 0.475, 0.189], - [0.231, 0.116, 0.477, 0.176], - [0.54, 0.111, 0.173, 0.176], - [0.214, 0.117, 0.147, 0.521], - [0.544, 0.12, 0.142, 0.194], - [0.586, 0.127, 0.112, 0.174], - [0.58, 0.122, 0.154, 0.144], - [0.39, 0.118, 0.344, 0.149], - [0.634, 0.119, 0.116, 0.131], - [0.395, 0.134, 0.301, 0.17], - [0.307, 0.159, 0.17, 0.364], - [0.172, 0.563, 0.105, 0.16], - [0.654, 0.142, 0.094, 0.11], - [0.585, 0.141, 0.08, 0.194], - [0.152, 0.101, 0.682, 0.065], - [0.751, 0.026, 0.197, 0.026], - [0.195, 0.599, 0.073, 0.133], - [0.059, 0.767, 0.024, 0.15], - [0.065, 0.735, 0.021, 0.179], - [0.629, 0.129, 0.048, 0.194], - [0.402, 0.087, 0.168, 0.342], - [0.098, 0.374, 0.204, 0.325], - [0.232, 0.043, 0.336, 0.39], - [0.39, 0.016, 0.537, 0.057], - [0.008, 0.046, 0.05, 0.896], - [0.284, 0.236, 0.274, 0.206], - [0.006, 0.002, 0.001, 0.991], - [0.001, 0.001, 0.97, 0.029], - [0.002, 0.811, 0.005, 0.182], - [0.004, 0.035, 0.002, 0.958], - [0.01, 0.001, 0.978, 0.011], - [0.012, 0.487, 0.046, 0.455], - [0.214, 0.506, 0.021, 0.259], - [0.064, 0.048, 0.083, 0.805], - [0.32, 0.134, 0.099, 0.447], - [0.046, 0.859, 0.033, 0.062], - [0.752, 0.136, 0.037, 0.075], - [0.553, 0.057, 0.279, 0.11], - [0.074, 0.09, 0.749, 0.087], - [0.749, 0.065, 0.111, 0.074], - [0.291, 0.082, 0.52, 0.107], - [0.706, 0.131, 0.065, 0.097], - [0.08, 0.71, 0.09, 0.121], - [0.204, 0.407, 0.078, 0.31], - [0.136, 0.583, 0.104, 0.177], - [0.662, 0.098, 0.11, 0.13], - [0.118, 0.33, 0.103, 0.45], - [0.112, 0.481, 0.097, 0.31], - [0.123, 0.109, 0.096, 0.671], - [0.185, 0.488, 0.109, 0.218], - [0.651, 0.114, 0.116, 0.118], - [0.161, 0.461, 0.132, 0.247], - [0.389, 0.217, 0.244, 0.149], - [0.134, 0.173, 0.122, 0.571], - ], - ZBTB26: [ - [0.012, 0.041, 0.141, 0.806], - [0.003, 0.984, 0.01, 0.004], - [0.013, 0.539, 0.08, 0.368], - [0.467, 0.033, 0.485, 0.014], - [0.006, 0.005, 0.985, 0.004], - [0.883, 0.034, 0.052, 0.03], - [0.506, 0.097, 0.264, 0.132], - ], - TAL1: [ - [0.075, 0.5, 0.219, 0.206], - [0.053, 0.048, 0.005, 0.894], - [0.098, 0.0, 0.0, 0.902], - [1.0, 0.0, 0.0, 0.0], - [0.001, 0.0, 0.0, 0.999], - [0.0, 1.0, 0.0, 0.0], - [0.321, 0.013, 0.017, 0.649], - ], - ELF2: [ - [0.514, 0.082, 0.269, 0.134], - [0.011, 0.777, 0.098, 0.114], - [0.036, 0.0, 0.0, 0.964], - [0.001, 0.0, 0.003, 0.996], - [0.0, 0.971, 0.013, 0.016], - [0.009, 0.97, 0.0, 0.022], - [0.026, 0.025, 0.611, 0.338], - [0.032, 0.228, 0.638, 0.102], - ], - NANOG: [ - [0.05, 0.485, 0.191, 0.274], - [0.084, 0.459, 0.107, 0.349], - [0.43, 0.051, 0.06, 0.459], - [0.023, 0.042, 0.033, 0.902], - [0.074, 0.007, 0.035, 0.884], - [0.092, 0.299, 0.553, 0.056], - [0.353, 0.015, 0.062, 0.57], - [0.254, 0.246, 0.141, 0.358], - [0.742, 0.039, 0.083, 0.136], - [0.048, 0.045, 0.05, 0.857], - [0.013, 0.007, 0.754, 0.226], - [0.037, 0.547, 0.127, 0.289], - [0.615, 0.021, 0.084, 0.281], - [0.651, 0.031, 0.191, 0.127], - [0.737, 0.054, 0.089, 0.121], - [0.165, 0.143, 0.167, 0.524], - ], - ONECUT2: [ - [0.145, 0.115, 0.057, 0.683], - [0.994, 0.001, 0.003, 0.002], - [0.148, 0.012, 0.014, 0.826], - [0.228, 0.002, 0.089, 0.68], - [0.0, 0.0, 1.0, 0.0], - [0.961, 0.01, 0.026, 0.003], - [0.017, 0.04, 0.016, 0.927], - [0.019, 0.071, 0.041, 0.869], - [0.23, 0.081, 0.076, 0.614], - ], - GLIS3: [ - [0.409, 0.198, 0.393, 0.0], - [0.023, 0.834, 0.003, 0.14], - [0.002, 0.971, 0.009, 0.018], - [0.102, 0.622, 0.002, 0.274], - [0.0, 0.997, 0.0, 0.002], - [0.103, 0.887, 0.003, 0.006], - [0.158, 0.526, 0.01, 0.306], - [0.393, 0.004, 0.578, 0.025], - [0.01, 0.759, 0.222, 0.009], - [0.356, 0.216, 0.24, 0.189], - [0.218, 0.139, 0.468, 0.176], - [0.405, 0.188, 0.275, 0.132], - [0.011, 0.163, 0.761, 0.065], - ], - ZFX: [ - [0.145, 0.484, 0.07, 0.301], - [0.119, 0.348, 0.325, 0.208], - [0.389, 0.133, 0.41, 0.068], - [0.001, 0.0, 0.985, 0.015], - [0.002, 0.0, 0.992, 0.006], - [0.006, 0.993, 0.0, 0.001], - [0.0, 0.998, 0.0, 0.002], - [0.005, 0.076, 0.0, 0.919], - [0.245, 0.209, 0.365, 0.181], - [0.054, 0.384, 0.454, 0.109], - ], - RBPJ: [ - [0.006, 0.212, 0.015, 0.767], - [0.0, 0.003, 0.0, 0.996], - [0.0, 1.0, 0.0, 0.0], - [0.063, 0.741, 0.0, 0.196], - [0.001, 0.987, 0.011, 0.0], - [0.775, 0.0, 0.188, 0.037], - [0.023, 0.437, 0.375, 0.165], - [0.257, 0.254, 0.407, 0.083], - [0.236, 0.35, 0.372, 0.042], - ], - ZNF680: [ - [0.198, 0.036, 0.711, 0.055], - [0.295, 0.184, 0.259, 0.262], - [0.09, 0.764, 0.03, 0.116], - [0.309, 0.564, 0.026, 0.102], - [0.792, 0.01, 0.166, 0.032], - [0.672, 0.005, 0.253, 0.07], - [0.001, 0.001, 0.998, 0.0], - [0.998, 0.001, 0.001, 0.0], - [0.946, 0.003, 0.035, 0.016], - [0.161, 0.002, 0.828, 0.009], - [0.996, 0.002, 0.002, 0.0], - [0.472, 0.288, 0.039, 0.201], - [0.041, 0.152, 0.03, 0.776], - [0.291, 0.138, 0.258, 0.312], - [0.626, 0.086, 0.077, 0.211], - [0.3, 0.036, 0.598, 0.067], - ], - } - \ No newline at end of file +export const MOTIFS = { + IRF1: [ + [0.323, 0.103, 0.503, 0.071], + [0.536, 0.179, 0.258, 0.028], + [0.818, 0.09, 0.058, 0.034], + [0.906, 0.0, 0.077, 0.017], + [0.182, 0.427, 0.213, 0.178], + [0.256, 0.242, 0.113, 0.39], + [0.1, 0.003, 0.898, 0.0], + [0.696, 0.3, 0.0, 0.004], + [0.837, 0.129, 0.005, 0.029], + [0.885, 0.0, 0.069, 0.046], + [0.082, 0.426, 0.46, 0.032], + [0.119, 0.292, 0.166, 0.423], + [0.422, 0.034, 0.486, 0.058], + [0.493, 0.145, 0.317, 0.045], + [0.511, 0.206, 0.151, 0.131], + [0.52, 0.098, 0.297, 0.085], + ], + HIC1: [ + [0.001, 0.022, 0.0, 0.977], + [0.06, 0.0, 0.938, 0.002], + [0.186, 0.783, 0.031, 0.0], + [0.007, 0.959, 0.002, 0.032], + [0.054, 0.934, 0.006, 0.006], + [0.261, 0.0, 0.169, 0.569], + [0.078, 0.487, 0.179, 0.255], + ], + LHX2: [ + [0.067, 0.666, 0.193, 0.074], + [0.0, 0.215, 0.0, 0.785], + [0.512, 0.446, 0.0, 0.041], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 0.003, 0.997], + [0.001, 0.018, 0.004, 0.978], + [0.988, 0.0, 0.0, 0.012], + ], + ZNF667: [ + [0.052, 0.058, 0.825, 0.064], + [0.236, 0.282, 0.331, 0.15], + [0.071, 0.083, 0.285, 0.561], + [0.074, 0.046, 0.816, 0.064], + [0.785, 0.012, 0.166, 0.037], + [0.083, 0.009, 0.902, 0.006], + [0.003, 0.936, 0.012, 0.049], + [0.028, 0.046, 0.025, 0.902], + [0.003, 0.448, 0.012, 0.537], + [0.123, 0.058, 0.12, 0.699], + [0.083, 0.028, 0.067, 0.822], + [0.758, 0.031, 0.117, 0.095], + [0.798, 0.117, 0.055, 0.031], + [0.393, 0.028, 0.518, 0.061], + [0.025, 0.043, 0.911, 0.021], + [0.077, 0.644, 0.187, 0.092], + [0.11, 0.788, 0.058, 0.043], + [0.518, 0.181, 0.086, 0.215], + [0.113, 0.712, 0.08, 0.095], + ], + ZNF341: [ + [0.008, 0.006, 0.977, 0.008], + [0.014, 0.961, 0.017, 0.009], + [0.047, 0.15, 0.053, 0.751], + [0.093, 0.309, 0.558, 0.041], + [0.027, 0.055, 0.01, 0.908], + [0.003, 0.069, 0.094, 0.834], + [0.075, 0.791, 0.088, 0.045], + [0.057, 0.685, 0.035, 0.223], + ], + TP53: [ + [0.264, 0.024, 0.526, 0.186], + [0.459, 0.0, 0.476, 0.066], + [0.017, 0.96, 0.001, 0.023], + [0.79, 0.0, 0.103, 0.106], + [0.209, 0.063, 0.019, 0.71], + [0.0, 0.004, 0.978, 0.018], + [0.055, 0.368, 0.0, 0.577], + [0.101, 0.59, 0.019, 0.289], + [0.156, 0.329, 0.136, 0.379], + [0.264, 0.177, 0.426, 0.133], + [0.251, 0.16, 0.411, 0.178], + [0.44, 0.054, 0.416, 0.09], + [0.079, 0.741, 0.153, 0.027], + [0.576, 0.225, 0.037, 0.162], + [0.269, 0.075, 0.137, 0.519], + [0.168, 0.078, 0.664, 0.09], + ], + SRF: [ + [0.258, 0.127, 0.089, 0.527], + [0.124, 0.132, 0.324, 0.419], + [0.261, 0.215, 0.293, 0.231], + [0.016, 0.968, 0.008, 0.008], + [0.0, 0.93, 0.0, 0.069], + [0.532, 0.061, 0.016, 0.39], + [0.251, 0.021, 0.017, 0.71], + [0.817, 0.009, 0.033, 0.141], + [0.131, 0.028, 0.004, 0.837], + [0.678, 0.016, 0.017, 0.29], + [0.353, 0.012, 0.061, 0.574], + [0.093, 0.0, 0.906, 0.001], + [0.032, 0.006, 0.951, 0.011], + [0.229, 0.294, 0.215, 0.262], + [0.419, 0.357, 0.109, 0.115], + [0.558, 0.077, 0.146, 0.219], + ], + SPIB: [ + [0.593, 0.068, 0.192, 0.148], + [0.602, 0.058, 0.23, 0.11], + [0.561, 0.029, 0.184, 0.227], + [0.182, 0.093, 0.697, 0.028], + [0.606, 0.102, 0.277, 0.015], + [0.088, 0.0, 0.904, 0.007], + [0.0, 0.004, 0.996, 0.0], + [0.991, 0.005, 0.001, 0.003], + [0.985, 0.0, 0.003, 0.012], + [0.052, 0.176, 0.769, 0.003], + [0.091, 0.076, 0.03, 0.803], + [0.076, 0.157, 0.738, 0.029], + ], + "NKX2-5": [ + [0.119, 0.154, 0.528, 0.2], + [0.172, 0.458, 0.144, 0.226], + [0.24, 0.026, 0.498, 0.236], + [0.247, 0.425, 0.163, 0.164], + [0.311, 0.187, 0.148, 0.353], + [0.316, 0.082, 0.427, 0.174], + [0.382, 0.249, 0.194, 0.175], + [0.147, 0.188, 0.406, 0.26], + [0.207, 0.307, 0.207, 0.279], + [0.31, 0.176, 0.316, 0.199], + [0.221, 0.319, 0.163, 0.296], + [0.087, 0.299, 0.176, 0.438], + [0.124, 0.206, 0.163, 0.507], + [0.205, 0.163, 0.216, 0.416], + [0.343, 0.07, 0.583, 0.004], + [0.987, 0.003, 0.003, 0.007], + [0.058, 0.019, 0.915, 0.007], + [0.404, 0.002, 0.021, 0.573], + [0.031, 0.002, 0.941, 0.027], + [0.055, 0.274, 0.541, 0.129], + ], + TBX5: [ + [0.195, 0.312, 0.018, 0.475], + [0.364, 0.131, 0.345, 0.16], + [0.008, 0.053, 0.099, 0.841], + [0.055, 0.745, 0.013, 0.187], + [0.615, 0.147, 0.039, 0.2], + [0.146, 0.427, 0.277, 0.149], + [0.333, 0.2, 0.078, 0.389], + [0.302, 0.273, 0.365, 0.059], + [0.547, 0.067, 0.144, 0.243], + [0.019, 0.929, 0.0, 0.052], + [0.816, 0.002, 0.081, 0.102], + [0.03, 0.834, 0.118, 0.017], + [0.168, 0.457, 0.068, 0.308], + [0.172, 0.192, 0.078, 0.558], + ], + ELK4: [ + [0.462, 0.116, 0.319, 0.103], + [0.008, 0.638, 0.097, 0.257], + [0.111, 0.0, 0.003, 0.887], + [0.002, 0.0, 0.0, 0.998], + [0.006, 0.994, 0.001, 0.0], + [0.005, 0.973, 0.0, 0.021], + [0.026, 0.021, 0.674, 0.279], + [0.053, 0.189, 0.653, 0.104], + ], + STAT3: [ + [0.082, 0.065, 0.078, 0.776], + [0.081, 0.012, 0.257, 0.649], + [0.192, 0.668, 0.07, 0.07], + [0.024, 0.748, 0.01, 0.218], + [0.313, 0.165, 0.35, 0.172], + [0.136, 0.003, 0.856, 0.005], + [0.03, 0.016, 0.819, 0.135], + [0.961, 0.028, 0.003, 0.008], + [0.964, 0.01, 0.022, 0.004], + ], + NR2F6: [ + [0.143, 0.125, 0.165, 0.567], + [0.12, 0.112, 0.629, 0.139], + [0.415, 0.123, 0.394, 0.068], + [0.484, 0.282, 0.129, 0.105], + [0.025, 0.949, 0.023, 0.003], + [0.015, 0.262, 0.028, 0.695], + [0.034, 0.196, 0.034, 0.736], + [0.007, 0.091, 0.001, 0.901], + [0.031, 0.012, 0.927, 0.03], + [0.44, 0.167, 0.271, 0.122], + [0.354, 0.392, 0.054, 0.199], + [0.05, 0.839, 0.046, 0.064], + [0.122, 0.363, 0.022, 0.493], + ], + FOXK2: [ + [0.028, 0.014, 0.014, 0.944], + [0.158, 0.004, 0.838, 0.0], + [0.003, 0.017, 0.017, 0.963], + [0.015, 0.0, 0.082, 0.903], + [0.002, 0.0, 0.126, 0.873], + [0.969, 0.007, 0.0, 0.023], + [0.0, 0.734, 0.016, 0.25], + ], + ZNF24: [ + [0.161, 0.533, 0.111, 0.195], + [0.415, 0.227, 0.193, 0.165], + [0.117, 0.311, 0.111, 0.461], + [0.172, 0.106, 0.163, 0.56], + [0.259, 0.569, 0.125, 0.047], + [0.527, 0.239, 0.131, 0.103], + [0.208, 0.089, 0.139, 0.564], + [0.056, 0.06, 0.085, 0.8], + [0.005, 0.968, 0.023, 0.004], + [0.878, 0.059, 0.037, 0.026], + [0.007, 0.149, 0.154, 0.69], + [0.059, 0.047, 0.082, 0.811], + [0.157, 0.656, 0.024, 0.163], + [0.572, 0.178, 0.178, 0.071], + [0.026, 0.091, 0.031, 0.851], + [0.036, 0.019, 0.044, 0.9], + [0.005, 0.984, 0.004, 0.007], + [0.568, 0.182, 0.149, 0.101], + ], + CEBPB: [ + [0.617, 0.049, 0.195, 0.139], + [0.0, 0.0, 0.0, 1.0], + [0.001, 0.0, 0.044, 0.955], + [0.332, 0.0, 0.286, 0.381], + [0.0, 0.998, 0.0, 0.002], + [0.65, 0.123, 0.001, 0.225], + [0.164, 0.363, 0.008, 0.466], + [0.716, 0.276, 0.0, 0.008], + [0.986, 0.001, 0.003, 0.01], + [0.021, 0.302, 0.136, 0.541], + ], + MAX: [ + [0.0, 1.0, 0.0, 0.0], + [0.96, 0.001, 0.018, 0.02], + [0.0, 0.481, 0.004, 0.515], + [0.031, 0.01, 0.96, 0.0], + [0.052, 0.154, 0.0, 0.795], + [0.0, 0.005, 0.92, 0.075], + ], + PPARG: [ + [0.098, 0.123, 0.08, 0.699], + [0.197, 0.143, 0.541, 0.119], + [0.57, 0.252, 0.129, 0.05], + [0.189, 0.72, 0.014, 0.077], + [0.05, 0.822, 0.007, 0.121], + [0.011, 0.161, 0.011, 0.816], + [0.075, 0.224, 0.037, 0.664], + [0.025, 0.061, 0.022, 0.893], + [0.132, 0.201, 0.536, 0.13], + [0.336, 0.316, 0.188, 0.159], + [0.065, 0.74, 0.043, 0.152], + [0.151, 0.727, 0.016, 0.107], + [0.063, 0.445, 0.046, 0.446], + [0.591, 0.145, 0.15, 0.114], + [0.214, 0.319, 0.335, 0.133], + [0.333, 0.09, 0.033, 0.544], + [0.196, 0.103, 0.152, 0.549], + ], + NFIA: [ + [0.057, 0.392, 0.103, 0.449], + [0.012, 0.19, 0.121, 0.677], + [0.045, 0.0, 0.847, 0.109], + [0.032, 0.063, 0.896, 0.009], + [0.286, 0.595, 0.041, 0.078], + [0.331, 0.204, 0.131, 0.334], + [0.206, 0.411, 0.171, 0.211], + [0.23, 0.209, 0.328, 0.234], + [0.187, 0.378, 0.239, 0.196], + [0.25, 0.105, 0.231, 0.413], + [0.042, 0.029, 0.746, 0.183], + [0.002, 0.93, 0.032, 0.035], + [0.0, 0.84, 0.0, 0.16], + [0.721, 0.027, 0.239, 0.013], + [0.37, 0.127, 0.454, 0.048], + ], + EPAS1: [ + [0.746, 0.021, 0.218, 0.015], + [0.002, 0.906, 0.001, 0.091], + [0.091, 0.0, 0.888, 0.021], + [0.004, 0.0, 0.004, 0.992], + [0.0, 0.0, 0.993, 0.007], + ], + JUNB: [ + [0.443, 0.231, 0.271, 0.055], + [0.0, 0.004, 0.001, 0.995], + [0.0, 0.0, 0.86, 0.14], + [0.991, 0.002, 0.0, 0.007], + [0.125, 0.375, 0.452, 0.047], + [0.0, 0.0, 0.0, 1.0], + [0.029, 0.971, 0.0, 0.0], + [0.992, 0.0, 0.008, 0.0], + [0.05, 0.31, 0.202, 0.438], + ], + PBX1: [ + [0.184, 0.032, 0.058, 0.727], + [0.002, 0.137, 0.86, 0.001], + [0.712, 0.16, 0.01, 0.118], + [0.071, 0.195, 0.361, 0.373], + [0.024, 0.001, 0.005, 0.971], + [0.016, 0.198, 0.783, 0.003], + [0.709, 0.001, 0.238, 0.053], + [0.008, 0.717, 0.053, 0.222], + [0.477, 0.004, 0.204, 0.315], + [0.127, 0.076, 0.584, 0.213], + ], + KLF13: [ + [0.098, 0.119, 0.721, 0.062], + [0.134, 0.693, 0.089, 0.084], + [0.11, 0.699, 0.064, 0.127], + [0.423, 0.562, 0.013, 0.001], + [0.002, 0.99, 0.0, 0.009], + [0.111, 0.0, 0.825, 0.065], + [0.0, 0.997, 0.0, 0.003], + [0.001, 0.98, 0.017, 0.003], + [0.049, 0.912, 0.001, 0.038], + [0.286, 0.555, 0.001, 0.158], + [0.027, 0.693, 0.071, 0.209], + ], + ZNF652: [ + [0.015, 0.024, 0.065, 0.896], + [0.006, 0.013, 0.023, 0.958], + [0.837, 0.019, 0.085, 0.058], + [0.949, 0.015, 0.022, 0.014], + [0.01, 0.98, 0.006, 0.004], + [0.034, 0.644, 0.031, 0.291], + [0.122, 0.712, 0.084, 0.082], + [0.095, 0.196, 0.063, 0.646], + [0.097, 0.111, 0.123, 0.669], + [0.14, 0.164, 0.181, 0.515], + [0.282, 0.383, 0.229, 0.106], + [0.286, 0.282, 0.189, 0.242], + [0.224, 0.185, 0.233, 0.357], + [0.162, 0.225, 0.304, 0.309], + [0.218, 0.254, 0.289, 0.239], + [0.176, 0.539, 0.115, 0.17], + ], + "NKX2-1": [ + [0.215, 0.012, 0.773, 0.001], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.002, 0.955, 0.042], + [0.349, 0.001, 0.0, 0.651], + [0.0, 0.0, 0.993, 0.007], + [0.004, 0.004, 0.713, 0.279], + ], + BACH1: [ + [0.015, 0.025, 0.121, 0.839], + [0.081, 0.013, 0.827, 0.079], + [0.72, 0.246, 0.006, 0.027], + [0.196, 0.002, 0.749, 0.054], + [0.005, 0.0, 0.008, 0.988], + [0.039, 0.907, 0.0, 0.054], + [0.915, 0.0, 0.056, 0.029], + [0.036, 0.263, 0.323, 0.377], + ], + HOXA9: [ + [0.209, 0.012, 0.025, 0.754], + [0.115, 0.014, 0.802, 0.068], + [0.974, 0.006, 0.009, 0.011], + [0.028, 0.008, 0.028, 0.935], + [0.085, 0.008, 0.049, 0.858], + [0.077, 0.072, 0.162, 0.689], + [0.978, 0.001, 0.02, 0.002], + [0.027, 0.152, 0.042, 0.779], + 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[0.064, 0.048, 0.083, 0.805], + [0.32, 0.134, 0.099, 0.447], + [0.046, 0.859, 0.033, 0.062], + [0.752, 0.136, 0.037, 0.075], + [0.553, 0.057, 0.279, 0.11], + [0.074, 0.09, 0.749, 0.087], + [0.749, 0.065, 0.111, 0.074], + [0.291, 0.082, 0.52, 0.107], + [0.706, 0.131, 0.065, 0.097], + [0.08, 0.71, 0.09, 0.121], + [0.204, 0.407, 0.078, 0.31], + [0.136, 0.583, 0.104, 0.177], + [0.662, 0.098, 0.11, 0.13], + [0.118, 0.33, 0.103, 0.45], + [0.112, 0.481, 0.097, 0.31], + [0.123, 0.109, 0.096, 0.671], + [0.185, 0.488, 0.109, 0.218], + [0.651, 0.114, 0.116, 0.118], + [0.161, 0.461, 0.132, 0.247], + [0.389, 0.217, 0.244, 0.149], + [0.134, 0.173, 0.122, 0.571], + ], + ZBTB26: [ + [0.012, 0.041, 0.141, 0.806], + [0.003, 0.984, 0.01, 0.004], + [0.013, 0.539, 0.08, 0.368], + [0.467, 0.033, 0.485, 0.014], + [0.006, 0.005, 0.985, 0.004], + [0.883, 0.034, 0.052, 0.03], + [0.506, 0.097, 0.264, 0.132], + ], + TAL1: [ + [0.075, 0.5, 0.219, 0.206], + [0.053, 0.048, 0.005, 0.894], + [0.098, 0.0, 0.0, 0.902], + [1.0, 0.0, 0.0, 0.0], + [0.001, 0.0, 0.0, 0.999], + [0.0, 1.0, 0.0, 0.0], + [0.321, 0.013, 0.017, 0.649], + ], + ELF2: [ + [0.514, 0.082, 0.269, 0.134], + [0.011, 0.777, 0.098, 0.114], + [0.036, 0.0, 0.0, 0.964], + [0.001, 0.0, 0.003, 0.996], + [0.0, 0.971, 0.013, 0.016], + [0.009, 0.97, 0.0, 0.022], + [0.026, 0.025, 0.611, 0.338], + [0.032, 0.228, 0.638, 0.102], + ], + NANOG: [ + [0.05, 0.485, 0.191, 0.274], + [0.084, 0.459, 0.107, 0.349], + [0.43, 0.051, 0.06, 0.459], + [0.023, 0.042, 0.033, 0.902], + [0.074, 0.007, 0.035, 0.884], + [0.092, 0.299, 0.553, 0.056], + [0.353, 0.015, 0.062, 0.57], + [0.254, 0.246, 0.141, 0.358], + [0.742, 0.039, 0.083, 0.136], + [0.048, 0.045, 0.05, 0.857], + [0.013, 0.007, 0.754, 0.226], + [0.037, 0.547, 0.127, 0.289], + [0.615, 0.021, 0.084, 0.281], + [0.651, 0.031, 0.191, 0.127], + [0.737, 0.054, 0.089, 0.121], + [0.165, 0.143, 0.167, 0.524], + ], + ONECUT2: [ + [0.145, 0.115, 0.057, 0.683], + [0.994, 0.001, 0.003, 0.002], + [0.148, 0.012, 0.014, 0.826], + [0.228, 0.002, 0.089, 0.68], + [0.0, 0.0, 1.0, 0.0], + [0.961, 0.01, 0.026, 0.003], + [0.017, 0.04, 0.016, 0.927], + [0.019, 0.071, 0.041, 0.869], + [0.23, 0.081, 0.076, 0.614], + ], + GLIS3: [ + [0.409, 0.198, 0.393, 0.0], + [0.023, 0.834, 0.003, 0.14], + [0.002, 0.971, 0.009, 0.018], + [0.102, 0.622, 0.002, 0.274], + [0.0, 0.997, 0.0, 0.002], + [0.103, 0.887, 0.003, 0.006], + [0.158, 0.526, 0.01, 0.306], + [0.393, 0.004, 0.578, 0.025], + [0.01, 0.759, 0.222, 0.009], + [0.356, 0.216, 0.24, 0.189], + [0.218, 0.139, 0.468, 0.176], + [0.405, 0.188, 0.275, 0.132], + [0.011, 0.163, 0.761, 0.065], + ], + ZFX: [ + [0.145, 0.484, 0.07, 0.301], + [0.119, 0.348, 0.325, 0.208], + [0.389, 0.133, 0.41, 0.068], + [0.001, 0.0, 0.985, 0.015], + [0.002, 0.0, 0.992, 0.006], + [0.006, 0.993, 0.0, 0.001], + [0.0, 0.998, 0.0, 0.002], + [0.005, 0.076, 0.0, 0.919], + [0.245, 0.209, 0.365, 0.181], + [0.054, 0.384, 0.454, 0.109], + ], + RBPJ: [ + [0.006, 0.212, 0.015, 0.767], + [0.0, 0.003, 0.0, 0.996], + [0.0, 1.0, 0.0, 0.0], + [0.063, 0.741, 0.0, 0.196], + [0.001, 0.987, 0.011, 0.0], + [0.775, 0.0, 0.188, 0.037], + [0.023, 0.437, 0.375, 0.165], + [0.257, 0.254, 0.407, 0.083], + [0.236, 0.35, 0.372, 0.042], + ], + ZNF680: [ + [0.198, 0.036, 0.711, 0.055], + [0.295, 0.184, 0.259, 0.262], + [0.09, 0.764, 0.03, 0.116], + [0.309, 0.564, 0.026, 0.102], + [0.792, 0.01, 0.166, 0.032], + [0.672, 0.005, 0.253, 0.07], + [0.001, 0.001, 0.998, 0.0], + [0.998, 0.001, 0.001, 0.0], + [0.946, 0.003, 0.035, 0.016], + [0.161, 0.002, 0.828, 0.009], + [0.996, 0.002, 0.002, 0.0], + [0.472, 0.288, 0.039, 0.201], + [0.041, 0.152, 0.03, 0.776], + [0.291, 0.138, 0.258, 0.312], + [0.626, 0.086, 0.077, 0.211], + [0.3, 0.036, 0.598, 0.067], + ], +} diff --git a/screen2.0/src/app/search/gbview/biosampletracks.tsx b/screen2.0/src/app/search/gbview/biosampletracks.tsx index cadc0e35..c03d1c01 100644 --- a/screen2.0/src/app/search/gbview/biosampletracks.tsx +++ b/screen2.0/src/app/search/gbview/biosampletracks.tsx @@ -1,226 +1,176 @@ -import { gql, useQuery } from "@apollo/client"; -import { associateBy } from "queryz"; -import { BigWigData, BigBedData, BigZoomData } from "bigwig-reader"; -import React, { RefObject, useEffect, useMemo, useState } from "react"; -import { DenseBigBed, EmptyTrack, FullBigWig } from "umms-gb"; -import { - BigRequest, - RequestError, -} from "umms-gb/dist/components/tracks/trackset/types"; -import { ValuedPoint } from "umms-gb/dist/utils/types"; -import { client } from "../ccredetails/client" -import CCRETooltip from "./ccretooltip" -import { TitledTrack } from "./defaulttracks"; - -type GenomicRange = { - chromosome?: string; - start: number; - end: number; - }; - -type BiosampleTracksProps = { - tracks: [string, string, string][]; - biosample: string; - domain: GenomicRange; - onHeightChanged?: (i: number) => void; - cCREHighlight?: GenomicRange; - cCREHighlights?: Set; - svgRef?: RefObject; - assembly: string; - oncCREClicked?: (accession: string) => void; - oncCREMousedOver?: (coordinates?: GenomicRange) => void; - oncCREMousedOut?: () => void; - onSettingsClick?: () => void; - }; - - - -export type BigResponseData = - | BigWigData[] - | BigBedData[] - | BigZoomData[] - | ValuedPoint[]; - -export type BigResponse = { - data: BigResponseData; - error: RequestError; -}; - -export type BigQueryResponse = { - bigRequests: BigResponse[]; -}; -export const BIG_QUERY = gql` - query BigRequests($bigRequests: [BigRequest!]!) { - bigRequests(requests: $bigRequests) { - data - error { - errortype - message - } - } - } -`; - -export const COLOR_MAP : Map = - new Map([ - [ - "DNase", - "#06da93" - - ], - [ - "H3K4me3", - "#ff0000" - - ] - , - [ - "H3K27ac", - "#ffcd00" - - ], - [ - "CTCF", - "#00b0d0" - - ] - ]); - - export const BIOSAMPLE_QUERY = gql` - query q ($assembly: String!) { - ccREBiosampleQuery(assembly: $assembly) { - biosamples { - name - dnase: experimentAccession(assay: "DNase") - h3k4me3: experimentAccession(assay: "H3K4me3") - h3k27ac: experimentAccession(assay: "H3K27ac") - ctcf: experimentAccession(assay: "CTCF") - dnase_signal: fileAccession(assay: "DNase") - h3k4me3_signal: fileAccession(assay: "H3K4me3") - h3k27ac_signal: fileAccession(assay: "H3K27ac") - ctcf_signal: fileAccession(assay: "CTCF") - } - } - } - ` -export const BiosampleTracks:React.FC = (props) => { - const [cTracks, setTracks] = useState<[string, string, string][]>(props.tracks) - - useEffect(()=>{ - setTracks(props.tracks) - },[props.tracks]) - const height = useMemo(() => cTracks && cTracks.length * 80, [cTracks]); - const bigRequests = useMemo( - () => - cTracks && cTracks.map((x) => ({ - chr1: props.domain.chromosome!, - start: props.domain.start, - end: props.domain.end, - preRenderedWidth: 1400, - url: x[1], - })), - [cTracks, props] - ); - const { data, loading } = useQuery(BIG_QUERY, { - variables: { bigRequests }, - client, - skip: bigRequests===null - - }); - const { data: biosampleData, loading: biosampleDataLoading } = useQuery(BIOSAMPLE_QUERY, { - variables: { assembly: "grch38" }, - client - }); - const groupedBiosamples = useMemo( - () => - associateBy( - biosampleData && biosampleData.ccREBiosampleQuery ? biosampleData.ccREBiosampleQuery.biosamples : [], - (x: any) => x.name as any, - (x) => x - ), - [biosampleData,biosampleDataLoading] - ) - console.log(groupedBiosamples.get(props.biosample)) - const cCRECoordinateMap = useMemo( - () => - associateBy( - (data && data.bigRequests && data.bigRequests[0].data) || [], - (x) => x.name, - (x) => ({ chromosome: x.chr, start: x.start, end: x.end }) - ), - [data] - ) - useEffect(() => { - height && props.onHeightChanged && props.onHeightChanged(height); - }, [props.onHeightChanged, height, props]); - - const [settingsMousedOver, setSettingsMousedOver] = useState(false); - const [settingsModalShown, setSettingsModalShown] = useState(false); - - return loading || !cTracks || !height || (data?.bigRequests.length || 0) < 2 ? ( - - ) : ( - <> - - - - {(data?.bigRequests || []).map((data, i) => ( - - ))} - - - - {settingsMousedOver && ( - - )} - - setSettingsMousedOver(true)} - onMouseOut={() => setSettingsMousedOver(false)} - strokeWidth={1} - transform="translate(20,0)" - onClick={() => { - props.onSettingsClick && props.onSettingsClick(); - setSettingsModalShown(true); - }} - /> - - Biosample-Specific Tracks - - - ); -} \ No newline at end of file +import { gql, useQuery } from "@apollo/client" +import { associateBy } from "queryz" +import { BigWigData, BigBedData, BigZoomData } from "bigwig-reader" +import React, { RefObject, useEffect, useMemo, useState } from "react" +import { EmptyTrack } from "umms-gb" +import { RequestError } from "umms-gb/dist/components/tracks/trackset/types" +import { ValuedPoint } from "umms-gb/dist/utils/types" +import { client } from "../ccredetails/client" +import { TitledTrack } from "./defaulttracks" + +type GenomicRange = { + chromosome?: string + start: number + end: number +} + +type BiosampleTracksProps = { + tracks: [string, string, string][] + biosample: string + domain: GenomicRange + onHeightChanged?: (i: number) => void + cCREHighlight?: GenomicRange + cCREHighlights?: Set + svgRef?: RefObject + assembly: string + oncCREClicked?: (accession: string) => void + oncCREMousedOver?: (coordinates?: GenomicRange) => void + oncCREMousedOut?: () => void + onSettingsClick?: () => void +} + +export type BigResponseData = BigWigData[] | BigBedData[] | BigZoomData[] | ValuedPoint[] + +export type BigResponse = { + data: BigResponseData + error: RequestError +} + +export type BigQueryResponse = { + bigRequests: BigResponse[] +} +export const BIG_QUERY = gql` + query BigRequests($bigRequests: [BigRequest!]!) { + bigRequests(requests: $bigRequests) { + data + error { + errortype + message + } + } + } +` + +export const COLOR_MAP: Map = new Map([ + ["DNase", "#06da93"], + ["H3K4me3", "#ff0000"], + ["H3K27ac", "#ffcd00"], + ["CTCF", "#00b0d0"], +]) + +export const BIOSAMPLE_QUERY = gql` + query q($assembly: String!) { + ccREBiosampleQuery(assembly: $assembly) { + biosamples { + name + dnase: experimentAccession(assay: "DNase") + h3k4me3: experimentAccession(assay: "H3K4me3") + h3k27ac: experimentAccession(assay: "H3K27ac") + ctcf: experimentAccession(assay: "CTCF") + dnase_signal: fileAccession(assay: "DNase") + h3k4me3_signal: fileAccession(assay: "H3K4me3") + h3k27ac_signal: fileAccession(assay: "H3K27ac") + ctcf_signal: fileAccession(assay: "CTCF") + } + } + } +` +export const BiosampleTracks: React.FC = (props) => { + const [cTracks, setTracks] = useState<[string, string, string][]>(props.tracks) + + useEffect(() => { + setTracks(props.tracks) + }, [props.tracks]) + const height = useMemo(() => cTracks && cTracks.length * 80, [cTracks]) + const bigRequests = useMemo( + () => + cTracks && + cTracks.map((x) => ({ + chr1: props.domain.chromosome!, + start: props.domain.start, + end: props.domain.end, + preRenderedWidth: 1400, + url: x[1], + })), + [cTracks, props] + ) + const { data, loading } = useQuery(BIG_QUERY, { + variables: { bigRequests }, + client, + skip: bigRequests === null, + }) + const { data: biosampleData, loading: biosampleDataLoading } = useQuery(BIOSAMPLE_QUERY, { + variables: { assembly: props.assembly.toLowerCase() }, + client, + }) + const groupedBiosamples = useMemo( + () => + associateBy( + biosampleData && biosampleData.ccREBiosampleQuery ? biosampleData.ccREBiosampleQuery.biosamples : [], + (x: any) => x.name as any, + (x) => x + ), + [biosampleData, biosampleDataLoading] + ) + + const cCRECoordinateMap = useMemo( + () => + associateBy( + (data && data.bigRequests && data.bigRequests[0].data) || [], + (x) => x.name, + (x) => ({ chromosome: x.chr, start: x.start, end: x.end }) + ), + [data] + ) + useEffect(() => { + height && props.onHeightChanged && props.onHeightChanged(height) + }, [props.onHeightChanged, height, props]) + + const [settingsMousedOver, setSettingsMousedOver] = useState(false) + + return loading || !cTracks || !height || (data?.bigRequests.length || 0) < 2 ? ( + + ) : ( + <> + + + + {(data?.bigRequests || []).map((data, i) => ( + + ))} + + + + {settingsMousedOver && } + + setSettingsMousedOver(true)} + onMouseOut={() => setSettingsMousedOver(false)} + strokeWidth={1} + transform="translate(20,0)" + /> + + Biosample-Specific Tracks + + + ) +} diff --git a/screen2.0/src/app/search/gbview/ccretooltip.tsx b/screen2.0/src/app/search/gbview/ccretooltip.tsx index b8475ff1..2450c173 100644 --- a/screen2.0/src/app/search/gbview/ccretooltip.tsx +++ b/screen2.0/src/app/search/gbview/ccretooltip.tsx @@ -1,95 +1,95 @@ -import { gql, useQuery } from "@apollo/client" -import React, { useMemo } from "react" -import { CircularProgress } from "@mui/material" -import { client } from "../ccredetails/client" - -export const COLORS = new Map([ - ["PLS", "#ff0000"], - ["pELS", "#ffa700"], - ["dELS", "#ffcd00"], - ["DNase-H3K4me3", "#ffaaaa"], - ["CTCF-only", "#00b0f0"], -]) - -export const GROUPS = new Map([ - ["PLS", "promoter-like"], - ["pELS", "proximal enhancer-like"], - ["dELS", "distal enhancer-like"], - ["DNase-H3K4me3", "DNase-H3K4me3"], - ["CTCF-only", "CTCF-only"], -]) - -const QUERY = gql` - query cCRE($assembly: String!, $accession: [String!], $experiments: [String!]) { - cCREQuery(assembly: $assembly, accession: $accession) { - group - zScores(experiments: $experiments) { - experiment - score - } - } - } -` - -const MAXZ_QUERY = gql` - query cCRE($assembly: String!, $accession: [String!]) { - cCREQuery(assembly: $assembly, accession: $accession) { - group - dnase: maxZ(assay: "dnase") - h3k4me3: maxZ(assay: "h3k4me3") - h3k27ac: maxZ(assay: "h3k27ac") - ctcf: maxZ(assay: "ctcf") - } - } -` - -const biosampleExperiments = (x) => [x.dnase, x.h3k4me3, x.h3k27ac, x.ctcf].filter((xx) => !!xx) - -const MARKS = ["DNase", "H3K4me3", "H3K27ac", "CTCF"] -const marks = (x) => [x.dnase, x.h3k4me3, x.h3k27ac, x.ctcf].map((x, i) => x && MARKS[i]).filter((xx) => !!xx) - -const CCRETooltip = (props) => { - const experiments = useMemo( - () => (props.biosample ? biosampleExperiments(props.biosample) : ["dnase", "h3k4me3", "h3k27ac", "ctcf"]), - [props] - ) - const { data, loading } = useQuery(props.biosample ? QUERY : MAXZ_QUERY, { - variables: { - assembly: props.assembly, - accession: props.name, - experiments, - }, - client - }) - return ( -
    - {loading || !data.cCREQuery[0] ? ( - - ) : ( - <> - - - - {props.name} ⸱ {GROUPS.get(data.cCREQuery[0].group || "")} - - - Click for details about this cCRE -
    -
    - {props.biosample ? "Z-scores in " + props.biosample.name : "Max Z-scores across all biosamples:"} -
    - {(props.biosample ? marks(props.biosample) : MARKS).map((x, i) => ( - - {x}:{" "} - {props.biosample - ? data.cCREQuery[0].zScores.find((xx) => xx.experiment === experiments[i]).score.toFixed(2) - : data.cCREQuery[0][experiments[i]].toFixed(2)} -
    -     - ))} - - )} -
    - ) -} -export default CCRETooltip +import { gql, useQuery } from "@apollo/client" +import React, { useMemo } from "react" +import { CircularProgress } from "@mui/material" +import { client } from "../ccredetails/client" + +export const COLORS = new Map([ + ["PLS", "#ff0000"], + ["pELS", "#ffa700"], + ["dELS", "#ffcd00"], + ["DNase-H3K4me3", "#ffaaaa"], + ["CTCF-only", "#00b0f0"], +]) + +export const GROUPS = new Map([ + ["PLS", "promoter-like"], + ["pELS", "proximal enhancer-like"], + ["dELS", "distal enhancer-like"], + ["DNase-H3K4me3", "DNase-H3K4me3"], + ["CTCF-only", "CTCF-only"], +]) + +const QUERY = gql` + query cCRE($assembly: String!, $accession: [String!], $experiments: [String!]) { + cCREQuery(assembly: $assembly, accession: $accession) { + group + zScores(experiments: $experiments) { + experiment + score + } + } + } +` + +const MAXZ_QUERY = gql` + query cCRE($assembly: String!, $accession: [String!]) { + cCREQuery(assembly: $assembly, accession: $accession) { + group + dnase: maxZ(assay: "dnase") + h3k4me3: maxZ(assay: "h3k4me3") + h3k27ac: maxZ(assay: "h3k27ac") + ctcf: maxZ(assay: "ctcf") + } + } +` + +const biosampleExperiments = (x) => [x.dnase, x.h3k4me3, x.h3k27ac, x.ctcf].filter((xx) => !!xx) + +const MARKS = ["DNase", "H3K4me3", "H3K27ac", "CTCF"] +const marks = (x) => [x.dnase, x.h3k4me3, x.h3k27ac, x.ctcf].map((x, i) => x && MARKS[i]).filter((xx) => !!xx) + +const CCRETooltip = (props) => { + const experiments = useMemo( + () => (props.biosample ? biosampleExperiments(props.biosample) : ["dnase", "h3k4me3", "h3k27ac", "ctcf"]), + [props] + ) + const { data, loading } = useQuery(props.biosample ? QUERY : MAXZ_QUERY, { + variables: { + assembly: props.assembly, + accession: props.name, + experiments, + }, + client, + }) + return ( +
    + {loading || !data.cCREQuery[0] ? ( + + ) : ( + <> + + + + {props.name} ⸱ {GROUPS.get(data.cCREQuery[0].group || "")} + + + Click for details about this cCRE +
    +
    + {props.biosample ? "Z-scores in " + props.biosample.name : "Max Z-scores across all biosamples:"} +
    + {(props.biosample ? marks(props.biosample) : MARKS).map((x, i) => ( + + {x}:{" "} + {props.biosample + ? data.cCREQuery[0].zScores.find((xx) => xx.experiment === experiments[i]).score.toFixed(2) + : data.cCREQuery[0][experiments[i]].toFixed(2)} +
    +     + ))} + + )} +
    + ) +} +export default CCRETooltip diff --git a/screen2.0/src/app/search/gbview/controls.tsx b/screen2.0/src/app/search/gbview/controls.tsx index 144ceb90..c018eb4f 100644 --- a/screen2.0/src/app/search/gbview/controls.tsx +++ b/screen2.0/src/app/search/gbview/controls.tsx @@ -1,39 +1,38 @@ -import React from 'react'; - -import ShiftButton from './shiftbutton'; -import ZoomButton from './zoombutton'; - -export interface Domain { - chromosome?: string; - start: number; - end: number; -}; -export type ControlProps = { - domain: Domain; - onDomainChanged: (domain: Domain) => void; - -}; -const Controls = ({ domain, onDomainChanged }) => { - return( - <> - move  - - - - - -   - zoom in  - - -   - zoom out  - - - - - -
    - -)}; -export default Controls; \ No newline at end of file +import React from "react" + +import ShiftButton from "./shiftbutton" +import ZoomButton from "./zoombutton" + +export interface Domain { + chromosome?: string + start: number + end: number +} +export type ControlProps = { + domain: Domain + onDomainChanged: (domain: Domain) => void +} +const Controls = ({ domain, onDomainChanged }) => { + return ( + <> + move  + + + + + + +   zoom in  + + + +   zoom out  + + + + +
    + + ) +} +export default Controls diff --git a/screen2.0/src/app/search/gbview/cytobandview.tsx b/screen2.0/src/app/search/gbview/cytobandview.tsx index 0bfa6902..c2b633e6 100644 --- a/screen2.0/src/app/search/gbview/cytobandview.tsx +++ b/screen2.0/src/app/search/gbview/cytobandview.tsx @@ -1,91 +1,85 @@ -import React, { useMemo } from "react"; -import { gql, useQuery } from "@apollo/client"; -import { Cytobands } from "umms-gb"; -import { Grid } from "@mui/material"; -import { client } from "../ccredetails/client" -export type GenomicRange = { - chromosome?: string; - start: number; - end: number; - }; - -const CYTOBAND_QUERY = gql` - query cytobands($assembly: String!, $chromosome: String) { - cytoband(assembly: $assembly, chromosome: $chromosome) { - stain - coordinates { - chromosome - start - end - } - } - } -`; - -export type CytobandQueryResponse = { - cytoband: { - stain: string; - coordinates: { - chromosome: string; - start: number; - end: number; - }; - }[]; -}; - -export type CytobandsProps = { - assembly: string; - chromosome: string; - innerWidth: number; - height: number; - position?: GenomicRange; -}; - -const CytobandView: React.FC = (props) => { - const { loading, data } = useQuery(CYTOBAND_QUERY, { - variables: { - assembly: props.assembly, - chromosome: props.chromosome, - }, - fetchPolicy: "cache-and-network", - nextFetchPolicy: "cache-first", - client, - }); - const domain = useMemo( - () => - data && { - start: 0, - end: Math.max( - ...(data.cytoband.length === 0 - ? [1] - : data.cytoband.map((x) => x.coordinates.end)) - ), - }, - [data] - ); - return loading || !data ? null : ( - - - - - - - - - - {props.assembly}:{props.chromosome} - - - - ); -}; -export default CytobandView; +import React, { useMemo } from "react" +import { gql, useQuery } from "@apollo/client" +import { Cytobands } from "umms-gb" +import { Grid } from "@mui/material" +import { client } from "../ccredetails/client" +export type GenomicRange = { + chromosome?: string + start: number + end: number +} + +const CYTOBAND_QUERY = gql` + query cytobands($assembly: String!, $chromosome: String) { + cytoband(assembly: $assembly, chromosome: $chromosome) { + stain + coordinates { + chromosome + start + end + } + } + } +` + +export type CytobandQueryResponse = { + cytoband: { + stain: string + coordinates: { + chromosome: string + start: number + end: number + } + }[] +} + +export type CytobandsProps = { + assembly: string + chromosome: string + innerWidth: number + height: number + position?: GenomicRange +} + +const CytobandView: React.FC = (props) => { + const { loading, data } = useQuery(CYTOBAND_QUERY, { + variables: { + assembly: props.assembly, + chromosome: props.chromosome, + }, + fetchPolicy: "cache-and-network", + nextFetchPolicy: "cache-first", + client, + }) + const domain = useMemo( + () => + data && { + start: 0, + end: Math.max(...(data.cytoband.length === 0 ? [1] : data.cytoband.map((x) => x.coordinates.end))), + }, + [data] + ) + return loading || !data ? null : ( + + + + + + + + + + {props.assembly}:{props.chromosome} + + + + ) +} +export default CytobandView diff --git a/screen2.0/src/app/search/gbview/defaulttracks.tsx b/screen2.0/src/app/search/gbview/defaulttracks.tsx index 1a9827e0..73431831 100644 --- a/screen2.0/src/app/search/gbview/defaulttracks.tsx +++ b/screen2.0/src/app/search/gbview/defaulttracks.tsx @@ -1,366 +1,217 @@ -import { gql, useQuery } from "@apollo/client"; -import { associateBy } from "queryz" -import { BigWigData, BigBedData, BigZoomData } from "bigwig-reader"; -import React, { RefObject, useEffect, useMemo, useState } from "react"; -import { DenseBigBed, EmptyTrack, FullBigWig } from "umms-gb"; -import { - BigRequest, - RequestError, -} from "umms-gb/dist/components/tracks/trackset/types"; -import { ValuedPoint } from "umms-gb/dist/utils/types"; -import { client } from "../ccredetails/client" -import CCRETooltip from "./ccretooltip" -/* -export const DEFAULT_TRACKS = ( - assembly: string -): Map => { - console.log -return assembly.toLowerCase() === "mm10" - ? new Map([ - ["All cCREs colored by group", { url: `gs://gcp.wenglab.org/${assembly}-cCREs.bigBed` }], - ["Aggregated DNase-seq signal, all Registry biosamples", { url: `gs://gcp.wenglab.org/dnase.${assembly}.sum.bigWig` }], - ]) : - new Map([ - [ - "All cCREs colored by group", - { - url: "gs://gcp.wenglab.org/GRCh38-cCREs.bigBed", - }, - ], - [ - "Aggregated DNase-seq signal, all Registry biosamples", - { - url: "gs://gcp.wenglab.org/dnase.GRCh38.sum.bigWig", - }, - ], - [ - "Aggregated H3K4me3 ChIP-seq signal, all Registry biosamples", - { - url: "gs://gcp.wenglab.org/h3k4me3.hg38.sum.bigWig", - }, - ] - , - [ - "Aggregated H3K27ac ChIP-seq signal, all Registry biosamples", - { - url: "gs://gcp.wenglab.org/h3k27ac.hg38.sum.bigWig", - }, - ], - [ - "Aggregated CTCF ChIP-seq signal, all Registry biosamples", - { - url: "gs://gcp.wenglab.org/ctcf.hg38.sum.bigWig", - }, - ] - - ]); -} - -export const TRACK_ORDER = (assembly) => {return assembly.toLowerCase() === "mm10" ? [ "All cCREs colored by group", -"Aggregated DNase-seq signal, all Registry biosamples"] -:[ - "All cCREs colored by group", - "Aggregated DNase-seq signal, all Registry biosamples", - "Aggregated H3K4me3 ChIP-seq signal, all Registry biosamples", - "Aggregated H3K27ac ChIP-seq signal, all Registry biosamples", - "Aggregated CTCF ChIP-seq signal, all Registry biosamples" - -]}; - -export const tracks = (assembly: string, pos: GenomicRange) => - TRACK_ORDER(assembly).map((x) => ({ - chr1: pos.chromosome!, - start: pos.start, - end: pos.end, - ...DEFAULT_TRACKS(assembly).get(x)!, - preRenderedWidth: 1400, - })); -*/ -export const BIG_QUERY = gql` - query BigRequests($bigRequests: [BigRequest!]!) { - bigRequests(requests: $bigRequests) { - data - error { - errortype - message - } - } - } -`; - -export const COLOR_MAP : Map = - new Map([ - [ - "Aggregated DNase-seq signal, all Registry biosamples", - "#06da93" - - ], - [ - "Aggregated H3K4me3 ChIP-seq signal, all Registry biosamples", - "#ff0000" - - ] - , - [ - "Aggregated H3K27ac ChIP-seq signal, all Registry biosamples", - "#ffcd00" - - ], - [ - "Aggregated CTCF ChIP-seq signal, all Registry biosamples", - "#00b0d0" - - ] - ]); - -type GenomicRange = { - chromosome?: string; - start: number; - end: number; -}; - -export type BigResponseData = - | BigWigData[] - | BigBedData[] - | BigZoomData[] - | ValuedPoint[]; - -export type BigResponse = { - data: BigResponseData; - error: RequestError -}; - -export type BigQueryResponse = { - bigRequests: BigResponse[]; -}; - -type DefaultTracksProps = { - //tracks: BigRequest[]; - domain: GenomicRange; - onHeightChanged?: (i: number) => void; - cCREHighlight?: GenomicRange; - cCREHighlights?: Set; - svgRef?: RefObject; - assembly: string; - oncCREClicked?: (accession: string) => void; - oncCREMousedOver?: (coordinates?: GenomicRange) => void; - oncCREMousedOut?: () => void; - onSettingsClick?: () => void; -}; - -export const TitledTrack: React.FC<{ - data: BigResponseData; - assembly: string; - url: string; - title: string; - color?: string; - height: number; - transform?: string; - onHeightChanged?: (height: number) => void; - domain: GenomicRange; - svgRef?: React.RefObject; - oncCREMousedOver?: (coordinates?: GenomicRange) => void; - oncCREMousedOut?: () => void; - cCRECoordinateMap?: any; - biosample?: string -}> = ({ - data, - assembly, - url, - title, - height, - domain, - transform, - onHeightChanged, - svgRef, - color, - oncCREMousedOver, - oncCREMousedOut, - cCRECoordinateMap, - biosample -}) => { - useEffect( - () => onHeightChanged && onHeightChanged(height + 40), - [height, onHeightChanged] - ); - console.log(color,title) - return ( - - - {(url.endsWith(".bigBed") || url.endsWith(".bigbed")) ? ( - } - onMouseOver={(x) => oncCREMousedOver && x.name && oncCREMousedOver(cCRECoordinateMap.get(x.name))} - onMouseOut={oncCREMousedOut} - /> - ) : ( - - )} - - ); -}; - -const DefaultTracks: React.FC = (props) => { - - const [cTracks, setTracks] = useState<[string, string][]>( props.assembly.toLowerCase()==='mm10' ? [ - [ - "All cCREs colored by group", - "gs://gcp.wenglab.org/mm10-cCREs.bigBed", - - ], - [ - "Aggregated DNase-seq signal, all Registry biosamples", - "gs://gcp.wenglab.org/dnase.mm10.sum.bigWig", - - - ], - ] : [ - [ - "All cCREs colored by group", - "gs://gcp.wenglab.org/GRCh38-cCREs.bigBed", - - ], - [ - "Aggregated DNase-seq signal, all Registry biosamples", - "gs://gcp.wenglab.org/dnase.GRCh38.sum.bigWig", - - ], - [ - "Aggregated H3K4me3 ChIP-seq signal, all Registry biosamples", - "gs://gcp.wenglab.org/h3k4me3.hg38.sum.bigWig", - - ] - , - [ - "Aggregated H3K27ac ChIP-seq signal, all Registry biosamples", - "gs://gcp.wenglab.org/h3k27ac.hg38.sum.bigWig", - - ], - [ - "Aggregated CTCF ChIP-seq signal, all Registry biosamples", - "gs://gcp.wenglab.org/ctcf.hg38.sum.bigWig", - - ] - ]); - const height = useMemo(() => cTracks.length * 80, [cTracks]); - const bigRequests = useMemo( - () => - cTracks.map((x) => ({ - chr1: props.domain.chromosome!, - start: props.domain.start, - end: props.domain.end, - preRenderedWidth: 1400, - url: x[1], - })), - [cTracks, props] - ); - const { data, loading } = useQuery(BIG_QUERY, { - variables: { bigRequests }, - client - }); - const cCRECoordinateMap = useMemo( - () => - associateBy( - (data && data.bigRequests && data.bigRequests[0].data) || [], - (x) => x.name, - (x) => ({ chromosome: x.chr, start: x.start, end: x.end }) - ), - [data] - ) - useEffect(() => { - props.onHeightChanged && props.onHeightChanged(height); - }, [props.onHeightChanged, height, props]); - - const [settingsMousedOver, setSettingsMousedOver] = useState(false); - const [settingsModalShown, setSettingsModalShown] = useState(false); - - return loading || (data?.bigRequests.length || 0) < 2 ? ( - - ) : ( - <> - - - - {(data?.bigRequests || []).map((data, i) => ( - - ))} - - - - {settingsMousedOver && ( - - )} - - setSettingsMousedOver(true)} - onMouseOut={() => setSettingsMousedOver(false)} - strokeWidth={1} - transform="translate(20,0)" - onClick={() => { - props.onSettingsClick && props.onSettingsClick(); - setSettingsModalShown(true); - }} - /> - - Aggregated signal Tracks - - - ); -}; -export default DefaultTracks; +import { gql, useQuery } from "@apollo/client" +import { associateBy } from "queryz" +import { BigWigData, BigBedData, BigZoomData } from "bigwig-reader" +import React, { RefObject, useEffect, useMemo, useState } from "react" +import { DenseBigBed, EmptyTrack, FullBigWig } from "umms-gb" +import { RequestError } from "umms-gb/dist/components/tracks/trackset/types" +import { ValuedPoint } from "umms-gb/dist/utils/types" +import { client } from "../ccredetails/client" +import CCRETooltip from "./ccretooltip" + +export const BIG_QUERY = gql` + query BigRequests($bigRequests: [BigRequest!]!) { + bigRequests(requests: $bigRequests) { + data + error { + errortype + message + } + } + } +` + +export const COLOR_MAP: Map = new Map([ + ["Aggregated DNase-seq signal, all Registry biosamples", "#06da93"], + ["Aggregated H3K4me3 ChIP-seq signal, all Registry biosamples", "#ff0000"], + ["Aggregated H3K27ac ChIP-seq signal, all Registry biosamples", "#ffcd00"], + ["Aggregated CTCF ChIP-seq signal, all Registry biosamples", "#00b0d0"], +]) + +type GenomicRange = { + chromosome?: string + start: number + end: number +} + +export type BigResponseData = BigWigData[] | BigBedData[] | BigZoomData[] | ValuedPoint[] + +export type BigResponse = { + data: BigResponseData + error: RequestError +} + +export type BigQueryResponse = { + bigRequests: BigResponse[] +} + +type DefaultTracksProps = { + domain: GenomicRange + onHeightChanged?: (i: number) => void + cCREHighlight?: GenomicRange + cCREHighlights?: Set + svgRef?: RefObject + assembly: string + oncCREClicked?: (accession: string) => void + oncCREMousedOver?: (coordinates?: GenomicRange) => void + oncCREMousedOut?: () => void + onSettingsClick?: () => void +} + +export const TitledTrack: React.FC<{ + data: BigResponseData + assembly: string + url: string + title: string + color?: string + height: number + transform?: string + onHeightChanged?: (height: number) => void + domain: GenomicRange + svgRef?: React.RefObject + oncCREMousedOver?: (coordinates?: GenomicRange) => void + oncCREMousedOut?: () => void + cCRECoordinateMap?: any + biosample?: string +}> = ({ + data, + assembly, + url, + title, + height, + domain, + transform, + onHeightChanged, + svgRef, + color, + oncCREMousedOver, + oncCREMousedOut, + cCRECoordinateMap, + biosample, +}) => { + useEffect(() => onHeightChanged && onHeightChanged(height + 40), [height, onHeightChanged]) + + return ( + + + {url.endsWith(".bigBed") || url.endsWith(".bigbed") ? ( + } + onMouseOver={(x) => oncCREMousedOver && x.name && oncCREMousedOver(cCRECoordinateMap.get(x.name))} + onMouseOut={oncCREMousedOut} + /> + ) : ( + + )} + + ) +} + +const DefaultTracks: React.FC = (props) => { + const [cTracks, setTracks] = useState<[string, string][]>( + props.assembly.toLowerCase() === "mm10" + ? [ + ["All cCREs colored by group", "gs://gcp.wenglab.org/mm10-cCREs.bigBed"], + ["Aggregated DNase-seq signal, all Registry biosamples", "gs://gcp.wenglab.org/dnase.mm10.sum.bigWig"], + ] + : [ + ["All cCREs colored by group", "gs://gcp.wenglab.org/GRCh38-cCREs.bigBed"], + ["Aggregated DNase-seq signal, all Registry biosamples", "gs://gcp.wenglab.org/dnase.GRCh38.sum.bigWig"], + ["Aggregated H3K4me3 ChIP-seq signal, all Registry biosamples", "gs://gcp.wenglab.org/h3k4me3.hg38.sum.bigWig"], + ["Aggregated H3K27ac ChIP-seq signal, all Registry biosamples", "gs://gcp.wenglab.org/h3k27ac.hg38.sum.bigWig"], + ["Aggregated CTCF ChIP-seq signal, all Registry biosamples", "gs://gcp.wenglab.org/ctcf.hg38.sum.bigWig"], + ] + ) + const height = useMemo(() => cTracks.length * 80, [cTracks]) + const bigRequests = useMemo( + () => + cTracks.map((x) => ({ + chr1: props.domain.chromosome!, + start: props.domain.start, + end: props.domain.end, + preRenderedWidth: 1400, + url: x[1], + })), + [cTracks, props] + ) + const { data, loading } = useQuery(BIG_QUERY, { + variables: { bigRequests }, + client, + }) + const cCRECoordinateMap = useMemo( + () => + associateBy( + (data && data.bigRequests && data.bigRequests[0].data) || [], + (x) => x.name, + (x) => ({ chromosome: x.chr, start: x.start, end: x.end }) + ), + [data] + ) + useEffect(() => { + props.onHeightChanged && props.onHeightChanged(height) + }, [props.onHeightChanged, height, props]) + + const [settingsMousedOver, setSettingsMousedOver] = useState(false) + + return loading || (data?.bigRequests.length || 0) < 2 ? ( + + ) : ( + <> + + + + {(data?.bigRequests || []).map((data, i) => ( + + ))} + + + + {settingsMousedOver && } + + setSettingsMousedOver(true)} + onMouseOut={() => setSettingsMousedOver(false)} + strokeWidth={1} + transform="translate(20,0)" + /> + + Aggregated signal Tracks + + + ) +} +export default DefaultTracks diff --git a/screen2.0/src/app/search/gbview/egenetracks.tsx b/screen2.0/src/app/search/gbview/egenetracks.tsx index 1765673c..7e12d12c 100644 --- a/screen2.0/src/app/search/gbview/egenetracks.tsx +++ b/screen2.0/src/app/search/gbview/egenetracks.tsx @@ -1,102 +1,77 @@ - -import React, { useState } from "react"; -import { - EmptyTrack, - PackTranscriptTrack, - SquishTranscriptTrack, -} from "umms-gb"; -import { TranscriptList } from "umms-gb/dist/components/tracks/transcripts/types"; - -export type GenomicRange = { - chromosome?: string; - start: number; - end: number; -}; -export type EGeneTrackProps = { - expandedCoordinates: GenomicRange; - genes: TranscriptList[]; - highlights?: Set; - onSettingsClick?: () => void; - onHeightChanged?: (x: number) => void; - width?: number; - squish?: boolean; -}; - -const EGeneTracks: React.FC = (props) => { - const [settingsMousedOver, setSettingsMousedOver] = useState(false); - const [height, setHeight] = useState(60); - return ( - - - {props.squish ? ( - { - setHeight(x + 40); - props.onHeightChanged && props.onHeightChanged(40 + x); - }} - color="#880000" - /> - ) : ( - { - setHeight(x + 40); - props.onHeightChanged && props.onHeightChanged(40 + x); - }} - color="#880000" - /> - )} - {settingsMousedOver && ( - - )} - - setSettingsMousedOver(true)} - onMouseOut={() => setSettingsMousedOver(false)} - strokeWidth={1} - transform="translate(20,0)" - onClick={props.onSettingsClick} - /> - - Genes - - - ); -}; -export default EGeneTracks; +import React, { useState } from "react" +import { EmptyTrack, PackTranscriptTrack, SquishTranscriptTrack } from "umms-gb" +import { TranscriptList } from "umms-gb/dist/components/tracks/transcripts/types" + +export type GenomicRange = { + chromosome?: string + start: number + end: number +} +export type EGeneTrackProps = { + expandedCoordinates: GenomicRange + genes: TranscriptList[] + highlights?: Set + onSettingsClick?: () => void + onHeightChanged?: (x: number) => void + width?: number + squish?: boolean +} + +const EGeneTracks: React.FC = (props) => { + const [settingsMousedOver, setSettingsMousedOver] = useState(false) + const [height, setHeight] = useState(60) + return ( + + + {props.squish ? ( + { + setHeight(x + 40) + props.onHeightChanged && props.onHeightChanged(40 + x) + }} + color="#880000" + /> + ) : ( + { + setHeight(x + 40) + props.onHeightChanged && props.onHeightChanged(40 + x) + }} + color="#880000" + /> + )} + {settingsMousedOver && ( + + )} + + setSettingsMousedOver(true)} + onMouseOut={() => setSettingsMousedOver(false)} + strokeWidth={1} + transform="translate(20,0)" + onClick={props.onSettingsClick} + /> + + Genes + + + ) +} +export default EGeneTracks diff --git a/screen2.0/src/app/search/gbview/genomebrowserview.tsx b/screen2.0/src/app/search/gbview/genomebrowserview.tsx index 4e433de7..b56d92dd 100644 --- a/screen2.0/src/app/search/gbview/genomebrowserview.tsx +++ b/screen2.0/src/app/search/gbview/genomebrowserview.tsx @@ -1,241 +1,239 @@ -"use client" -import React, { useMemo, useState, useRef, useCallback, useEffect } from "react" -import Grid2 from "../../../common/mui-client-wrappers/Grid2" -import { RulerTrack, GenomeBrowser } from "umms-gb"; -import Controls from "./controls"; -import { gql, useQuery } from "@apollo/client"; -import CytobandView, { GenomicRange } from "./cytobandview" -import EGeneTracks from "./egenetracks"; -import { client } from "../ccredetails/client" -import DefaultTracks from "./defaulttracks"; -import {BiosampleTracks} from "./biosampletracks" -type GenomeBrowserViewProps = { - coordinates : { - start: number, - end: number, - chromosome?: string - }, - biosample?: string - gene?: string - assembly: string -} -const BIOSAMPLE_QUERY = gql` -query biosamples { - human: ccREBiosampleQuery(assembly: "grch38") { - biosamples { - name - dnase: experimentAccession(assay: "DNase") - h3k4me3: experimentAccession(assay: "H3K4me3") - h3k27ac: experimentAccession(assay: "H3K27ac") - ctcf: experimentAccession(assay: "CTCF") - dnase_signal: fileAccession(assay: "DNase") - h3k4me3_signal: fileAccession(assay: "H3K4me3") - h3k27ac_signal: fileAccession(assay: "H3K27ac") - ctcf_signal: fileAccession(assay: "CTCF") - } - } - mouse: ccREBiosampleQuery(assembly: "mm10") { - biosamples { - name - dnase: experimentAccession(assay: "DNase") - h3k4me3: experimentAccession(assay: "H3K4me3") - h3k27ac: experimentAccession(assay: "H3K27ac") - ctcf: experimentAccession(assay: "CTCF") - dnase_signal: fileAccession(assay: "DNase") - h3k4me3_signal: fileAccession(assay: "H3K4me3") - h3k27ac_signal: fileAccession(assay: "H3K27ac") - ctcf_signal: fileAccession(assay: "CTCF") - } - } -} -` -const GENE_QUERY = gql` - query s( - $chromosome: String - $start: Int - $end: Int - $assembly: String! - ) { - - gene( - chromosome: $chromosome - start: $start - end: $end - assembly: $assembly - ) { - name - strand - transcripts { - name - strand - exons { - coordinates { - chromosome - start - end - } - } - coordinates { - chromosome - start - end - } - } - } - } -`; -export type Transcript = { - id: string; - name: string; - strand: string; - coordinates: GenomicRange; -}; -export type SNPQueryResponse = { - gene: { - name: string; - strand: string; - transcripts: Transcript[]; - }[]; -}; -export function expandCoordinates(coordinates, l = 20000) { - return { - chromosome: coordinates.chromosome, - start: coordinates.start - l < 0 ? 0 : coordinates.start - l, - end: coordinates.end + l, - } - } - -export const GenomeBrowserView: React.FC = (props) =>{ - console.log(props.gene) - const svgRef = useRef(null); - const expandedCoordinates = useMemo(() => expandCoordinates(props.coordinates), [props.coordinates]) - const [coordinates, setCoordinates] = useState(expandedCoordinates); - const [highlight, setHighlight] = useState(null) - const [cTracks, setTracks] = useState<[string, string, string][]| null>(null) - const snpResponse = useQuery(GENE_QUERY, { - variables: { ...coordinates, assembly:props.assembly }, - fetchPolicy: "cache-and-network", - nextFetchPolicy: "cache-first", - client, - }); - - const groupedTranscripts = useMemo( - () => - snpResponse.data?.gene.map((x) => ({ - ...x, - transcripts: x.transcripts.map((xx) => ({ - ...xx, - color: props.gene ? (x).name.includes(props.gene) ? "#880000" : "#aaaaaa" : "#aaaaaa" - })), - })), - [snpResponse,props.gene] - ); - const onDomainChanged = useCallback( - (d: GenomicRange) => { - const chr = - d.chromosome === undefined - ? props.coordinates.chromosome - : d.chromosome; - const start = Math.round(d.start); - const end = Math.round(d.end); - if (end - start > 10) { - setCoordinates({ chromosome: chr, start, end }); - } - }, - [props.coordinates] - ); - const l = useCallback((c) => ((c - coordinates.start) * 1400) / (coordinates.end - coordinates.start), [coordinates]) - - const { loading: bloading, data : bdata } = useQuery(BIOSAMPLE_QUERY, { - fetchPolicy: "cache-and-network", - nextFetchPolicy: "cache-first", - client, - }); - useEffect(()=>{ - if(bdata && props.biosample) - { - const humanBiosamples = bdata && bdata.human && bdata.human.biosamples - const mouseBiosamples = bdata && bdata.mouse && bdata.mouse.biosamples - - const result = props.assembly==="mm10" ? mouseBiosamples.find(m=>m.name===props.biosample) : humanBiosamples.find(m=>m.name===props.biosample) - const r = [result.dnase_signal, result.h3k4me3_signal, result.h3k27ac_signal, result.ctcf_signal].filter((x) => !!x) - //copy v4 bed files to google bucket - const bigBedUrl = `https://downloads.wenglab.org/Registry-V4/${r.join("_")}.bigBed` - let tracks:[string, string, string][] = [[`cCREs colored by activity in ${props.biosample}`,bigBedUrl ,""]] - if(result.dnase_signal) tracks.push([`DNase-seq signal in ${props.biosample}`,`https://www.encodeproject.org/files/${result.dnase_signal}/@@download/${result.dnase_signal}.bigWig`,"DNase"]) - if(result.h3k4me3_signal) tracks.push([`H3K4me3 ChIP-seq signal in ${props.biosample}`,`https://www.encodeproject.org/files/${result.h3k4me3_signal}/@@download/${result.h3k4me3_signal}.bigWig`,"H3K4me3"]) - if(result.h3k27ac_signal) tracks.push([`H3K27ac ChIP-seq signal in ${props.biosample}`,`https://www.encodeproject.org/files/${result.h3k27ac_signal}/@@download/${result.h3k27ac_signal}.bigWig`,"H3K27ac"]) - if(result.ctcf_signal) tracks.push([`CTCF ChIP-seq signal in ${props.biosample}`,`https://www.encodeproject.org/files/${result.ctcf_signal}/@@download/${result.ctcf_signal}.bigWig`,"CTCF"]) - setTracks(tracks) - - } - - },[bdata,props.biosample]) - return(<> - -
    - -
    -
    - -
    -
    -
    - { - if (Math.ceil(x.end) - Math.floor(x.start) > 10) { - setCoordinates({ - chromosome: coordinates.chromosome, - start: Math.floor(x.start), - end: Math.ceil(x.end), - }); - } - }} - > - {highlight && ( - - )} - - = 500000 ? true: false } - /> - - x && setHighlight(x)} - oncCREMousedOut={() => setHighlight(null)} - /> - {props.biosample && props.assembly!="mm10" && cTracks && x && setHighlight(x)} - oncCREMousedOut={() => setHighlight(null)} - />} - - -     -     ) -} \ No newline at end of file +"use client" +import React, { useMemo, useState, useRef, useCallback, useEffect } from "react" +import Grid2 from "../../../common/mui-client-wrappers/Grid2" +import { RulerTrack, GenomeBrowser } from "umms-gb" +import Controls from "./controls" +import { gql, useQuery } from "@apollo/client" +import CytobandView, { GenomicRange } from "./cytobandview" +import EGeneTracks from "./egenetracks" +import { client } from "../ccredetails/client" +import DefaultTracks from "./defaulttracks" +import { BiosampleTracks } from "./biosampletracks" +type GenomeBrowserViewProps = { + coordinates: { + start: number + end: number + chromosome?: string + } + biosample?: string + gene?: string + assembly: string +} +const BIOSAMPLE_QUERY = gql` + query biosamples { + human: ccREBiosampleQuery(assembly: "grch38") { + biosamples { + name + dnase: experimentAccession(assay: "DNase") + h3k4me3: experimentAccession(assay: "H3K4me3") + h3k27ac: experimentAccession(assay: "H3K27ac") + ctcf: experimentAccession(assay: "CTCF") + dnase_signal: fileAccession(assay: "DNase") + h3k4me3_signal: fileAccession(assay: "H3K4me3") + h3k27ac_signal: fileAccession(assay: "H3K27ac") + ctcf_signal: fileAccession(assay: "CTCF") + } + } + mouse: ccREBiosampleQuery(assembly: "mm10") { + biosamples { + name + dnase: experimentAccession(assay: "DNase") + h3k4me3: experimentAccession(assay: "H3K4me3") + h3k27ac: experimentAccession(assay: "H3K27ac") + ctcf: experimentAccession(assay: "CTCF") + dnase_signal: fileAccession(assay: "DNase") + h3k4me3_signal: fileAccession(assay: "H3K4me3") + h3k27ac_signal: fileAccession(assay: "H3K27ac") + ctcf_signal: fileAccession(assay: "CTCF") + } + } + } +` +const GENE_QUERY = gql` + query s($chromosome: String, $start: Int, $end: Int, $assembly: String!) { + gene(chromosome: $chromosome, start: $start, end: $end, assembly: $assembly) { + name + strand + transcripts { + name + strand + exons { + coordinates { + chromosome + start + end + } + } + coordinates { + chromosome + start + end + } + } + } + } +` +export type Transcript = { + id: string + name: string + strand: string + coordinates: GenomicRange +} +export type SNPQueryResponse = { + gene: { + name: string + strand: string + transcripts: Transcript[] + }[] +} +export function expandCoordinates(coordinates, l = 20000) { + return { + chromosome: coordinates.chromosome, + start: coordinates.start - l < 0 ? 0 : coordinates.start - l, + end: coordinates.end + l, + } +} + +export const GenomeBrowserView: React.FC = (props) => { + console.log(props.gene) + const svgRef = useRef(null) + const expandedCoordinates = useMemo(() => expandCoordinates(props.coordinates), [props.coordinates]) + const [coordinates, setCoordinates] = useState(expandedCoordinates) + const [highlight, setHighlight] = useState(null) + const [cTracks, setTracks] = useState<[string, string, string][] | null>(null) + const snpResponse = useQuery(GENE_QUERY, { + variables: { ...coordinates, assembly: props.assembly }, + fetchPolicy: "cache-and-network", + nextFetchPolicy: "cache-first", + client, + }) + + const groupedTranscripts = useMemo( + () => + snpResponse.data?.gene.map((x) => ({ + ...x, + transcripts: x.transcripts.map((xx) => ({ + ...xx, + color: props.gene ? (x.name.includes(props.gene) ? "#880000" : "#aaaaaa") : "#aaaaaa", + })), + })), + [snpResponse, props.gene] + ) + const onDomainChanged = useCallback( + (d: GenomicRange) => { + const chr = d.chromosome === undefined ? props.coordinates.chromosome : d.chromosome + const start = Math.round(d.start) + const end = Math.round(d.end) + if (end - start > 10) { + setCoordinates({ chromosome: chr, start, end }) + } + }, + [props.coordinates] + ) + const l = useCallback((c) => ((c - coordinates.start) * 1400) / (coordinates.end - coordinates.start), [coordinates]) + + const { loading: bloading, data: bdata } = useQuery(BIOSAMPLE_QUERY, { + fetchPolicy: "cache-and-network", + nextFetchPolicy: "cache-first", + client, + }) + useEffect(() => { + if (bdata && props.biosample) { + const humanBiosamples = bdata && bdata.human && bdata.human.biosamples + const mouseBiosamples = bdata && bdata.mouse && bdata.mouse.biosamples + + const result = + props.assembly === "mm10" + ? mouseBiosamples.find((m) => m.name === props.biosample) + : humanBiosamples.find((m) => m.name === props.biosample) + const r = [result.dnase_signal, result.h3k4me3_signal, result.h3k27ac_signal, result.ctcf_signal].filter((x) => !!x) + //copy v4 bed files to google bucket + const bigBedUrl = `https://downloads.wenglab.org/Registry-V4/${r.join("_")}.bigBed` + let tracks: [string, string, string][] = [[`cCREs colored by activity in ${props.biosample}`, bigBedUrl, ""]] + if (result.dnase_signal) + tracks.push([ + `DNase-seq signal in ${props.biosample}`, + `https://www.encodeproject.org/files/${result.dnase_signal}/@@download/${result.dnase_signal}.bigWig`, + "DNase", + ]) + if (result.h3k4me3_signal) + tracks.push([ + `H3K4me3 ChIP-seq signal in ${props.biosample}`, + `https://www.encodeproject.org/files/${result.h3k4me3_signal}/@@download/${result.h3k4me3_signal}.bigWig`, + "H3K4me3", + ]) + if (result.h3k27ac_signal) + tracks.push([ + `H3K27ac ChIP-seq signal in ${props.biosample}`, + `https://www.encodeproject.org/files/${result.h3k27ac_signal}/@@download/${result.h3k27ac_signal}.bigWig`, + "H3K27ac", + ]) + if (result.ctcf_signal) + tracks.push([ + `CTCF ChIP-seq signal in ${props.biosample}`, + `https://www.encodeproject.org/files/${result.ctcf_signal}/@@download/${result.ctcf_signal}.bigWig`, + "CTCF", + ]) + setTracks(tracks) + } + }, [bdata, props.biosample]) + return ( + <> + + +
    + +
    +
    + +
    +
    +
    + { + if (Math.ceil(x.end) - Math.floor(x.start) > 10) { + setCoordinates({ + chromosome: coordinates.chromosome, + start: Math.floor(x.start), + end: Math.ceil(x.end), + }) + } + }} + > + {highlight && ( + + )} + + = 500000 ? true : false} + /> + + x && setHighlight(x)} + oncCREMousedOut={() => setHighlight(null)} + /> + {props.biosample && props.assembly != "mm10" && cTracks && ( + x && setHighlight(x)} + oncCREMousedOut={() => setHighlight(null)} + /> + )} + +     +     + + ) +} diff --git a/screen2.0/src/app/search/gbview/shiftbutton.tsx b/screen2.0/src/app/search/gbview/shiftbutton.tsx index dc20d4b6..45e16ea3 100644 --- a/screen2.0/src/app/search/gbview/shiftbutton.tsx +++ b/screen2.0/src/app/search/gbview/shiftbutton.tsx @@ -1,29 +1,32 @@ -import React from 'react'; -import { - Button - } from "@mui/material" -export interface Domain { - chromosome?: string; - start: number; - end: number; -}; - -export type ShiftButtonProps = { - text: string; - shift: number; - domain: Domain; - onClick: (domain: Domain) => void; -}; - -const ShiftButton= ({ text, shift, domain, onClick }) => { - return ( - <> - - - -)}; -export default ShiftButton; \ No newline at end of file +import React from "react" +import { Button } from "@mui/material" +export interface Domain { + chromosome?: string + start: number + end: number +} + +export type ShiftButtonProps = { + text: string + shift: number + domain: Domain + onClick: (domain: Domain) => void +} + +const ShiftButton = ({ text, shift, domain, onClick }) => { + return ( + <> + + + ) +} +export default ShiftButton diff --git a/screen2.0/src/app/search/gbview/tfmotiftrack.tsx b/screen2.0/src/app/search/gbview/tfmotiftrack.tsx index 48608674..90b3fcec 100644 --- a/screen2.0/src/app/search/gbview/tfmotiftrack.tsx +++ b/screen2.0/src/app/search/gbview/tfmotiftrack.tsx @@ -1,92 +1,75 @@ -import React, { useState, useRef } from "react"; -import { - EmptyTrack, - SquishBigBed -} from "umms-gb"; -import { DNALogo, Y } from "logots-react" -import {MOTIFS} from "./allmotifs" -import { Typography } from "@mui/material"; -export type GenomicRange = { - chromosome?: string; - start: number; - end: number; -}; - -const MotifTooltip = (props) => { - const rc = (x) => [...x].map((xx) => [...xx].reverse()).reverse() - return ( -
    - {props.rectname.split("$")[2]} - -
    - ) - } -export const TfMotifTrack = (props) => { - - const [height, setHeight] = useState(60); - const [settingsMousedOver, setSettingsMousedOver] = useState(false); - - return( - - { - setHeight(x + 40); - props.onHeightChanged && props.onHeightChanged(40 + x); - }} - data={props.data} - transform="translate(0,40)" - tooltipContent={(rect: any) => { console.log(rect,":recg"); return }} - onClick={(x: any) => { - //return window.open(`${x}`) - return window.open(`https://factorbook.org/tf/${props.assembly==="GRCh38" ? "human" : "mouse"}/${x.rectname.split("$")[2]}/motif`, "_blank") - } - } - /> - {settingsMousedOver && ( - - )} - - setSettingsMousedOver(true)} - onMouseOut={() => setSettingsMousedOver(false)} - strokeWidth={1} - transform="translate(20,0)" - onClick={props.onSettingsClick} - /> - - TF Binding sites - - ) -} \ No newline at end of file +import React, { useState, useRef } from "react" +import { EmptyTrack, SquishBigBed } from "umms-gb" +import { DNALogo, Y } from "logots-react" +import { MOTIFS } from "./allmotifs" +import { Typography } from "@mui/material" +export type GenomicRange = { + chromosome?: string + start: number + end: number +} + +const MotifTooltip = (props) => { + const rc = (x) => [...x].map((xx) => [...xx].reverse()).reverse() + return ( +
    + {props.rectname.split("$")[2]} + +
    + ) +} +export const TfMotifTrack = (props) => { + const [height, setHeight] = useState(60) + const [settingsMousedOver, setSettingsMousedOver] = useState(false) + + return ( + + + { + setHeight(x + 40) + props.onHeightChanged && props.onHeightChanged(40 + x) + }} + data={props.data} + transform="translate(0,40)" + tooltipContent={(rect: any) => { + console.log(rect, ":recg") + return + }} + onClick={(x: any) => { + //return window.open(`${x}`) + return window.open( + `https://factorbook.org/tf/${props.assembly === "GRCh38" ? "human" : "mouse"}/${x.rectname.split("$")[2]}/motif`, + "_blank" + ) + }} + /> + {settingsMousedOver && ( + + )} + + setSettingsMousedOver(true)} + onMouseOut={() => setSettingsMousedOver(false)} + strokeWidth={1} + transform="translate(20,0)" + onClick={props.onSettingsClick} + /> + + TF Binding sites + + + ) +} diff --git a/screen2.0/src/app/search/gbview/zoombutton.tsx b/screen2.0/src/app/search/gbview/zoombutton.tsx index fc0fb7f8..a7e09131 100644 --- a/screen2.0/src/app/search/gbview/zoombutton.tsx +++ b/screen2.0/src/app/search/gbview/zoombutton.tsx @@ -1,34 +1,31 @@ -import React from 'react'; -import { - Button - } from "@mui/material" -export interface Domain { - chromosome?: string; - start: number; - end: number; -}; -export type ZoomButtonProps = { - text: string; - factor: number; - domain: Domain; - onClick: (domain: Domain) => void; -}; - -const ZoomButton = ({ text, factor, domain, onClick }) => ( - -); -export default ZoomButton; \ No newline at end of file +import React from "react" +import { Button } from "@mui/material" +export interface Domain { + chromosome?: string + start: number + end: number +} +export type ZoomButtonProps = { + text: string + factor: number + domain: Domain + onClick: (domain: Domain) => void +} + +const ZoomButton = ({ text, factor, domain, onClick }) => ( + +) +export default ZoomButton diff --git a/screen2.0/src/common/components/MainResultsTable.tsx b/screen2.0/src/common/components/MainResultsTable.tsx index d748ac84..ece0c71d 100644 --- a/screen2.0/src/common/components/MainResultsTable.tsx +++ b/screen2.0/src/common/components/MainResultsTable.tsx @@ -3,26 +3,11 @@ import { usePathname, useRouter, useSearchParams } from "next/navigation" import { DataTable, DataTableProps, DataTableColumn } from "@weng-lab/psychscreen-ui-components" import React from "react" -import { Box, Button, Typography } from "@mui/material" -import Link from "next/link" -import { ObjectFlags } from "typescript" +import { Box, Typography } from "@mui/material" let COLUMNS = (rows) => { // can prob just use link instead here - const router = useRouter() - const pathname = usePathname() - const searchParams: any = useSearchParams()! - - const createQueryString = React.useCallback( - (name: string, value: string) => { - const params = new URLSearchParams(searchParams) - params.set(name, value) - - return params.toString() - }, - [searchParams] - ) - + let col: DataTableColumn[] = [ { header: "Accession", @@ -123,8 +108,7 @@ function MainResultsTable(props: Partial>) { }, [searchParams] ) - console.log(props.rows) - + return ( = (props: MainSearchProps) => { - const [value, setValue] = useState("") - const [checked, setChecked] = useState(props.initialChecked || false) - const [selectedSearch, setSelectedSearch] = useState("Genomic Region"); - const assembly = checked ? "mm10" : "GRCh38" - const handleSearchChange = (event: SelectChangeEvent) => { - - setSelectedSearch(event.target.value); - }; - const router = useRouter() - - const handleChange = (event: { target: { value: React.SetStateAction } }) => { - setValue(event.target.value) - } - - function handleSubmit() { - const assembly = checked ? "mm10" : "GRCh38" - //if submitted with empty value, use default search - if (value == "") { - router.push(`/search?assembly=${assembly}&chromosome=chr11&start=5205263&end=5381894`) - return - } - const input = value.split(":") - const chromosome = input[0] - const coordinates = input[1].split("-") - const start = coordinates[0] - const end = coordinates[1] - router.push(`/search?assembly=${assembly}&chromosome=${chromosome}&start=${start}&end=${end}`) - } - - return ( - - - - - - - - - {selectedSearch==="Genomic Region" ? { - if (event.code === "Enter") { - handleSubmit() - } - }} - InputProps={{ - endAdornment: ( - - handleSubmit()}> - - - - ), - }} - sx={{ mr: "1em", ml:"1em" }} - /> : selectedSearch==="Gene Name" ? : selectedSearch==="SNP rsID" ? : selectedSearch==="Cell Type"? : } - - - setChecked(checked)} - /> - - - - ) -} - -export default MainSearch diff --git a/screen2.0/src/common/components/ResponsiveAppBar.tsx b/screen2.0/src/common/components/ResponsiveAppBar.tsx index d655b1e6..c5c88151 100644 --- a/screen2.0/src/common/components/ResponsiveAppBar.tsx +++ b/screen2.0/src/common/components/ResponsiveAppBar.tsx @@ -1,46 +1,18 @@ "use client" import * as React from "react" - import { AppBar, Box, Toolbar, IconButton, Typography, Menu, Container, Button, MenuItem } from "@mui/material" import ArrowDropDownIcon from "@mui/icons-material/ArrowDropDown" import MenuIcon from "@mui/icons-material/Menu" - -import Grid2 from "@mui/material/Unstable_Grid2/Grid2" -import { - Autocomplete, - TextField, - Accordion, - AccordionDetails, - AccordionSummary, - debounce, - ButtonBase, - Checkbox, - FormControlLabel, - FormGroup, - ToggleButton, - ToggleButtonGroup, - Drawer, -} from "@mui/material" +import { Drawer } from "@mui/material" import CloseIcon from "@mui/icons-material/Close" import Divider from "@mui/material/Divider" -import ListItemButton from "@mui/material/ListItemButton" -import ListItemIcon from "@mui/material/ListItemIcon" -import ListItemText from "@mui/material/ListItemText" -import FolderIcon from "@mui/icons-material/Folder" -import ImageIcon from "@mui/icons-material/Image" -import DescriptionIcon from "@mui/icons-material/Description" -import InputBase from "@mui/material/InputBase" -import SearchIcon from "@mui/icons-material/Search" -import { ThemeProvider, createTheme } from "@mui/material/styles" - +import { ThemeProvider } from "@mui/material/styles" import Link from "next/link" import Image from "next/image" - -import HeaderSearch from "./HeaderSearch" - import nextConfig from "../../../next.config" import screenIcon from "../../../public/screenIcon.png" import { defaultTheme } from "../lib/themes" +import MainSearch from "./mainsearch/MainSearch" // CLICKING ON LINKS ONCE THE POPUP IS OPEN IS BROKEN!!! @@ -276,7 +248,7 @@ function ResponsiveAppBar() { {/* TODO onSubmit for search box */} - + {/* Settings */} diff --git a/screen2.0/src/common/components/CcreAutocomplete.tsx b/screen2.0/src/common/components/mainsearch/CcreAutocomplete.tsx similarity index 60% rename from screen2.0/src/common/components/CcreAutocomplete.tsx rename to screen2.0/src/common/components/mainsearch/CcreAutocomplete.tsx index 1898694c..350ef8d2 100644 --- a/screen2.0/src/common/components/CcreAutocomplete.tsx +++ b/screen2.0/src/common/components/mainsearch/CcreAutocomplete.tsx @@ -1,138 +1,154 @@ -"use client" -import * as React from "react"; -import Box from "@mui/material/Box"; -import TextField from "@mui/material/TextField"; -import Autocomplete from "@mui/material/Autocomplete"; -import Grid from "@mui/material/Grid"; -import Typography from "@mui/material/Typography"; -import { debounce } from "@mui/material/utils"; -import { Button } from "@weng-lab/psychscreen-ui-components"; -import { useRouter } from "next/navigation" - - ///search?assembly=GRCh38&chromosome=chr11&start=5205263&end=5381894&accession=EH38E1516972 - -const CCRE_AUTOCOMPLETE_QUERY = ` -query cCREQuery($accession_prefix: [String!], $limit: Int, $assembly: String!) { - cCREQuery(accession_prefix: $accession_prefix, assembly: $assembly, limit: $limit) { - accession - coordinates { - start - end - chromosome - } - } -} -`; -export const CcreAutoComplete = (props) => { - const [value, setValue] = React.useState(null); - const [inputValue, setInputValue] = React.useState(""); - const [options, setOptions] = React.useState([]); - const [ccreAccessions, setCcreAccessions] = React.useState([]); - - const router = useRouter() - const onSearchChange = async (value: any) => { - setOptions([]); - const response = await fetch("https://factorbook.api.wenglab.org/graphql", { - method: "POST", - body: JSON.stringify({ - query: CCRE_AUTOCOMPLETE_QUERY, - variables: { - assembly: props.assembly, - accession_prefix: [value], - limit: 100 - }, - }), - headers: { "Content-Type": "application/json" }, - }); - const ccreSuggestion = (await response.json()).data?.cCREQuery; - if (ccreSuggestion && ccreSuggestion.length > 0) { - const r = ccreSuggestion.map((g: any) => g.accession); - const ccres = ccreSuggestion.map((g: any) => { - return { - chrom: g.coordinates.chromosome, - start: g.coordinates.start, - end: g.coordinates.end, - ccreaccession: g.accession, - }; - }); - setOptions(r); - setCcreAccessions(ccres); - } else if (ccreSuggestion && ccreSuggestion.length === 0) { - setOptions([]); - setCcreAccessions([]); - } - }; - - const debounceFn = React.useCallback(debounce(onSearchChange, 500), []); - - return ( - - - { - if (event.key === "Enter") { - event.defaultPrevented = true; - - if (value) { - let chrom = ccreAccessions.find((g) => g.ccreaccession === value)?.chrom - let start = ccreAccessions.find((g) => g.ccreaccession === value)?.start - let end = ccreAccessions.find((g) => g.ccreaccession === value)?.end - router.push(`search?assembly=${props.assembly}&chromosome=${chrom}&start=${start}&end=${end}&accession=${value}`) - - } - } - }} - value={value} - onChange={(_: any, newValue: string | null) => { - setValue(newValue); - }} - - inputValue={inputValue} - onInputChange={(event, newInputValue) => { - if (newInputValue != "") { - debounceFn(newInputValue); - } - - setInputValue(newInputValue); - }} - noOptionsText="e.g. EH38E0001314" - renderInput={(params) => ( - - )} - renderOption={(props, option) => { - return ( -
  • - - - - {option} - - {ccreAccessions && ccreAccessions.find((g) => g.ccreaccession === option) && ( - - {`${ccreAccessions.find((g) => g.ccreaccession === option)?.chrom}:${ - ccreAccessions.find((g) => g.ccreaccession === option)?.start - }:${ccreAccessions.find((g) => g.ccreaccession === option)?.end}`} - - )} - - -
    • - ); - }} - /> -     - -     - ); -}; +"use client" +import * as React from "react" +import Box from "@mui/material/Box" +import TextField from "@mui/material/TextField" +import Autocomplete from "@mui/material/Autocomplete" +import Grid from "@mui/material/Grid" +import Typography from "@mui/material/Typography" +import { debounce } from "@mui/material/utils" +import { Button } from "@weng-lab/psychscreen-ui-components" +import { useRouter } from "next/navigation" + +///search?assembly=GRCh38&chromosome=chr11&start=5205263&end=5381894&accession=EH38E1516972 + +const CCRE_AUTOCOMPLETE_QUERY = ` +query cCREQuery($accession_prefix: [String!], $limit: Int, $assembly: String!) { + cCREQuery(accession_prefix: $accession_prefix, assembly: $assembly, limit: $limit) { + accession + coordinates { + start + end + chromosome + } + } +} +` +export const CcreAutoComplete = (props) => { + const [value, setValue] = React.useState(null) + const [inputValue, setInputValue] = React.useState("") + const [options, setOptions] = React.useState([]) + const [ccreAccessions, setCcreAccessions] = React.useState([]) + + const router = useRouter() + const onSearchChange = async (value: any) => { + setOptions([]) + const response = await fetch("https://factorbook.api.wenglab.org/graphql", { + method: "POST", + body: JSON.stringify({ + query: CCRE_AUTOCOMPLETE_QUERY, + variables: { + assembly: props.assembly, + accession_prefix: [value], + limit: 100, + }, + }), + headers: { "Content-Type": "application/json" }, + }) + const ccreSuggestion = (await response.json()).data?.cCREQuery + if (ccreSuggestion && ccreSuggestion.length > 0) { + const r = ccreSuggestion.map((g: any) => g.accession) + const ccres = ccreSuggestion.map((g: any) => { + return { + chrom: g.coordinates.chromosome, + start: g.coordinates.start, + end: g.coordinates.end, + ccreaccession: g.accession, + } + }) + setOptions(r) + setCcreAccessions(ccres) + } else if (ccreSuggestion && ccreSuggestion.length === 0) { + setOptions([]) + setCcreAccessions([]) + } + } + + const debounceFn = React.useCallback(debounce(onSearchChange, 500), []) + + return ( + + + { + if (event.key === "Enter") { + event.defaultPrevented = true + + if (value) { + let chrom = ccreAccessions.find((g) => g.ccreaccession === value)?.chrom + let start = ccreAccessions.find((g) => g.ccreaccession === value)?.start + let end = ccreAccessions.find((g) => g.ccreaccession === value)?.end + router.push(`search?assembly=${props.assembly}&chromosome=${chrom}&start=${start}&end=${end}&accession=${value}`) + } + } + }} + value={value} + onChange={(_: any, newValue: string | null) => { + setValue(newValue) + }} + inputValue={inputValue} + onInputChange={(event, newInputValue) => { + if (newInputValue != "") { + debounceFn(newInputValue) + } + + setInputValue(newInputValue) + }} + noOptionsText="e.g. EH38E0001314" + renderInput={(params) => ( + + )} + renderOption={(props, option) => { + return ( +
  • + + + + {option} + + {ccreAccessions && ccreAccessions.find((g) => g.ccreaccession === option) && ( + + {`${ccreAccessions.find((g) => g.ccreaccession === option)?.chrom}:${ + ccreAccessions.find((g) => g.ccreaccession === option)?.start + }:${ccreAccessions.find((g) => g.ccreaccession === option)?.end}`} + + )} + + +
    • + ) + }} + /> +     +     + ) +} diff --git a/screen2.0/src/common/components/CelltypeAutocomplete.tsx b/screen2.0/src/common/components/mainsearch/CelltypeAutocomplete.tsx similarity index 52% rename from screen2.0/src/common/components/CelltypeAutocomplete.tsx rename to screen2.0/src/common/components/mainsearch/CelltypeAutocomplete.tsx index f94bdda8..ba991f30 100644 --- a/screen2.0/src/common/components/CelltypeAutocomplete.tsx +++ b/screen2.0/src/common/components/mainsearch/CelltypeAutocomplete.tsx @@ -1,117 +1,136 @@ -import React, { useMemo, useState, useRef, useCallback, useEffect } from "react"; -import Box from "@mui/material/Box"; -import TextField from "@mui/material/TextField"; -import Autocomplete from "@mui/material/Autocomplete"; -import Grid from "@mui/material/Grid"; -import Typography from "@mui/material/Typography"; -import { debounce } from "@mui/material/utils"; -import { useRouter } from "next/navigation" -import { gql, useQuery } from "@apollo/client"; - -export const CelltypeAutocomplete = (props) => { - const [value, setValue] = useState(null); - const [inputValue, setInputValue] = useState(""); - const [options, setOptions] = useState([]); - const [cellTypes, setCelltypes] = useState([]); - const [loading, setLoading] = useState(false) - const router = useRouter() - - useEffect(() => { - fetch("https://downloads.wenglab.org/databyct.json") - .then((response) => { - - return response.json() - }) - .then((data) => { - //setCellTypes(data) - let byCt = Object.keys(data.byCellType).map(ct=>{ - return { - value: ct, - tissue: data.byCellType[ct][0].tissue, - biosample_summary: data.byCellType[ct][0].biosample_summary+":chr11:5205263-5381894", - } - }) - setOptions(byCt.map(ct=>ct.biosample_summary)) - setCelltypes(byCt) - setLoading(false) - }) - .catch((error: Error) => { - // logging - // throw error - }) - setLoading(true) - }, [props.assembly]) - - - - return ( - - - { - if (event.key === "Enter") { - event.defaultPrevented = true; - - if (value) { - - let tissue = cellTypes.find((g) => g.biosample_summary === value)?.tissue - let biosample = cellTypes.find((g) => g.biosample_summary === value)?.value - let biosample_summary = value.split(":")[0] - let chromosome = value.split(":")[1] - let start = value.split(":")[2].split("-")[0] - let end = value.split(":")[2].split("-")[1] - router.push(`search?assembly=${props.assembly}&chromosome=${chromosome}&start=${Math.max(0,start)}&end=${end}&BiosampleTissue=${tissue}&BiosampleSummary=${biosample_summary}&Biosample=${biosample}`) - } - } - }} - value={value} - onChange={(_: any, newValue: string | null) => { - setValue(newValue); - }} - inputValue={inputValue} - onInputChange={(event, newInputValue) => { - if (newInputValue != "") { - //debounceFn(newInputValue); - } - - setInputValue(newInputValue); - }} - noOptionsText="e.g. LNCAP" - renderInput={(params) => ( - - )} - renderOption={(props, option) => { - return ( -
  • - - - - {option} - - {cellTypes && cellTypes.find((g) => g.biosample_summary === option) && ( - - {`${cellTypes.find((g) => g.biosample_summary === option)?.tissue}`} - - )} - - -
    • - ); - }} - /> -     - -     - ); -}; +import React, { useMemo, useState, useRef, useCallback, useEffect } from "react" +import Box from "@mui/material/Box" +import TextField from "@mui/material/TextField" +import Autocomplete from "@mui/material/Autocomplete" +import Grid from "@mui/material/Grid" +import Typography from "@mui/material/Typography" +import { debounce } from "@mui/material/utils" +import { useRouter } from "next/navigation" +import { gql, useQuery } from "@apollo/client" + +export const CelltypeAutocomplete = (props) => { + const [value, setValue] = useState(null) + const [inputValue, setInputValue] = useState("") + const [options, setOptions] = useState([]) + const [cellTypes, setCelltypes] = useState([]) + const [loading, setLoading] = useState(false) + const router = useRouter() + + useEffect(() => { + fetch("https://downloads.wenglab.org/databyct.json") + .then((response) => { + return response.json() + }) + .then((data) => { + //setCellTypes(data) + let byCt = Object.keys(data.byCellType).map((ct) => { + return { + value: ct, + tissue: data.byCellType[ct][0].tissue, + biosample_summary: data.byCellType[ct][0].biosample_summary + ":chr11:5205263-5381894", + } + }) + setOptions(byCt.map((ct) => ct.biosample_summary)) + setCelltypes(byCt) + setLoading(false) + }) + .catch((error: Error) => { + // logging + // throw error + }) + setLoading(true) + }, [props.assembly]) + + return ( + + + { + if (event.key === "Enter") { + event.defaultPrevented = true + + if (value) { + let tissue = cellTypes.find((g) => g.biosample_summary === value)?.tissue + let biosample = cellTypes.find((g) => g.biosample_summary === value)?.value + let biosample_summary = value.split(":")[0] + let chromosome = value.split(":")[1] + let start = value.split(":")[2].split("-")[0] + let end = value.split(":")[2].split("-")[1] + router.push( + `search?assembly=${props.assembly}&chromosome=${chromosome}&start=${Math.max( + 0, + start + )}&end=${end}&BiosampleTissue=${tissue}&BiosampleSummary=${biosample_summary}&Biosample=${biosample}` + ) + } + } + }} + value={value} + onChange={(_: any, newValue: string | null) => { + setValue(newValue) + }} + inputValue={inputValue} + onInputChange={(event, newInputValue) => { + if (newInputValue != "") { + //debounceFn(newInputValue); + } + + setInputValue(newInputValue) + }} + noOptionsText="e.g. LNCAP" + renderInput={(params) => ( + + )} + renderOption={(props, option) => { + return ( +
  • + + + + {option} + + {cellTypes && cellTypes.find((g) => g.biosample_summary === option) && ( + + {`${cellTypes.find((g) => g.biosample_summary === option)?.tissue}`} + + )} + + +
    • + ) + }} + /> +     +     + ) +} diff --git a/screen2.0/src/common/components/GeneAutocomplete.tsx b/screen2.0/src/common/components/mainsearch/GeneAutocomplete.tsx similarity index 55% rename from screen2.0/src/common/components/GeneAutocomplete.tsx rename to screen2.0/src/common/components/mainsearch/GeneAutocomplete.tsx index 91a22f00..b7fe3123 100644 --- a/screen2.0/src/common/components/GeneAutocomplete.tsx +++ b/screen2.0/src/common/components/mainsearch/GeneAutocomplete.tsx @@ -1,198 +1,194 @@ -import * as React from "react"; -import Box from "@mui/material/Box"; -import TextField from "@mui/material/TextField"; -import Autocomplete from "@mui/material/Autocomplete"; -import Grid from "@mui/material/Grid"; -import Typography from "@mui/material/Typography"; -import { debounce } from "@mui/material/utils"; -import { useRouter } from "next/navigation" - -export type QueryResponse = [ - number, - string[], - any, - [string, string, string, string, string, string][], - string[] - ]; - -const GENE_AUTOCOMPLETE_QUERY = ` -query ($assembly: String!, $name_prefix: [String!], $limit: Int) { - gene(assembly: $assembly, name_prefix: $name_prefix, limit: $limit) { - name - id - coordinates { - start - chromosome - end - } - } - } - `; - -export const GeneAutoComplete = (props) => { - const [value, setValue] = React.useState(null); - const [inputValue, setInputValue] = React.useState(""); - const [options, setOptions] = React.useState([]); - const [geneids, setGeneIds] = React.useState< - { chrom: string; start: number; end: number; id: string; name: string }[] - >([]); - - const router = useRouter() - const [geneDesc, setgeneDesc] = - React.useState<{ name: string; desc: string }[]>(); - - React.useEffect(() => { - const fetchData = async () => { - let f = await Promise.all( - options.map((gene) => - fetch( - "https://clinicaltables.nlm.nih.gov/api/ncbi_genes/v3/search?authenticity_token=&terms=" + - gene.toUpperCase() - ) - .then((x) => x && x.json()) - .then((x) => { - const matches = - (x as QueryResponse)[3] && - (x as QueryResponse)[3].filter( - (x) => x[3] === gene.toUpperCase() - ); - return { - desc: - matches && matches.length >= 1 - ? matches[0][4] - : "(no description available)", - name: gene, - }; - }) - .catch(() => { - return { desc: "(no description available)", name: gene }; - }) - ) - ); - setgeneDesc(f); - }; - - options && fetchData(); - }, [options]); - - const onSearchChange = async (value: string) => { - setOptions([]); - const response = await fetch("https://ga.staging.wenglab.org/graphql", { - method: "POST", - body: JSON.stringify({ - query: GENE_AUTOCOMPLETE_QUERY, - variables: { - assembly: "GRCh38", - name_prefix: value, - limit: 1000, - }, - }), - headers: { "Content-Type": "application/json" }, - }); - const genesSuggestion = (await response.json()).data?.gene; - if (genesSuggestion && genesSuggestion.length > 0) { - const r = genesSuggestion.map((g) => g.name); - const g = genesSuggestion.map((g) => { - return { - chrom: g.coordinates.chromosome, - start: g.coordinates.start, - end: g.coordinates.end, - id: g.id, - name: g.name, - }; - }); - setOptions(r); - setGeneIds(g); - } else if (genesSuggestion && genesSuggestion.length === 0) { - setOptions([]); - setGeneIds([]); - } - }; - - const debounceFn = React.useCallback(debounce(onSearchChange, 500), []); - const gridsize = props.gridsize || 5.5; - return ( - - {props.showTitle && ( - - Search gene: -
    -     - )} - - { - if (event.key === "Enter") { - event.defaultPrevented = true; - console.log("value",value) - value && - props.onSelected && - props.onSelected({ - geneid: geneids - .find((g) => g.name === value) - ?.id.split(".")[0], - chromosome: geneids.find((g) => g.name === value)?.chrom, - start: geneids.find((g) => g.name === value)?.start, - end: geneids.find((g) => g.name === value)?.end, - }); - if (value) - { - let chrom = geneids.find((g) => g.name === value)?.chrom - let start = geneids.find((g) => g.name === value)?.start - let end = geneids.find((g) => g.name === value)?.end - router.push(`search?assembly=${props.assembly}&chromosome=${chrom}&start=${start}&end=${end}&gene=${value}`) - - } - - } - }} - value={value} - onChange={(_: any, newValue: string | null) => { - setValue(newValue); - }} - inputValue={inputValue} - onInputChange={(event, newInputValue) => { - if (newInputValue != "") { - debounceFn(newInputValue); - } - - setInputValue(newInputValue); - }} - noOptionsText="e.g sox4,gapdh" - renderInput={(params) => ( - - )} - renderOption={(props, option) => { - return ( -
  • - - - - {option} - - {geneDesc && geneDesc.find((g) => g.name === option) && ( - - {geneDesc.find((g) => g.name === option)?.desc} - - )} - - -
    • - ); - }} - /> -     -     - ); -}; +import * as React from "react" +import Box from "@mui/material/Box" +import TextField from "@mui/material/TextField" +import Autocomplete from "@mui/material/Autocomplete" +import Grid from "@mui/material/Grid" +import Typography from "@mui/material/Typography" +import { debounce } from "@mui/material/utils" +import { useRouter } from "next/navigation" +import SearchIcon from "@mui/icons-material/Search" +import { IconButton, InputAdornment, InputBaseProps, createTheme } from "@mui/material" +export type QueryResponse = [number, string[], any, [string, string, string, string, string, string][], string[]] + +const GENE_AUTOCOMPLETE_QUERY = ` +query ($assembly: String!, $name_prefix: [String!], $limit: Int) { + gene(assembly: $assembly, name_prefix: $name_prefix, limit: $limit) { + name + id + coordinates { + start + chromosome + end + } + } + } + ` + +export const GeneAutoComplete = (props) => { + const [value, setValue] = React.useState(null) + const [inputValue, setInputValue] = React.useState("") + const [options, setOptions] = React.useState([]) + const [geneids, setGeneIds] = React.useState<{ chrom: string; start: number; end: number; id: string; name: string }[]>([]) + + const router = useRouter() + const [geneDesc, setgeneDesc] = React.useState<{ name: string; desc: string }[]>() + + React.useEffect(() => { + const fetchData = async () => { + let f = await Promise.all( + options.map((gene) => + fetch("https://clinicaltables.nlm.nih.gov/api/ncbi_genes/v3/search?authenticity_token=&terms=" + gene.toUpperCase()) + .then((x) => x && x.json()) + .then((x) => { + const matches = (x as QueryResponse)[3] && (x as QueryResponse)[3].filter((x) => x[3] === gene.toUpperCase()) + return { + desc: matches && matches.length >= 1 ? matches[0][4] : "(no description available)", + name: gene, + } + }) + .catch(() => { + return { desc: "(no description available)", name: gene } + }) + ) + ) + setgeneDesc(f) + } + + options && fetchData() + }, [options]) + + const onSearchChange = async (value: string) => { + setOptions([]) + const response = await fetch("https://ga.staging.wenglab.org/graphql", { + method: "POST", + body: JSON.stringify({ + query: GENE_AUTOCOMPLETE_QUERY, + variables: { + assembly: "GRCh38", + name_prefix: value, + limit: 1000, + }, + }), + headers: { "Content-Type": "application/json" }, + }) + const genesSuggestion = (await response.json()).data?.gene + if (genesSuggestion && genesSuggestion.length > 0) { + const r = genesSuggestion.map((g) => g.name) + const g = genesSuggestion.map((g) => { + return { + chrom: g.coordinates.chromosome, + start: g.coordinates.start, + end: g.coordinates.end, + id: g.id, + name: g.name, + } + }) + setOptions(r) + setGeneIds(g) + } else if (genesSuggestion && genesSuggestion.length === 0) { + setOptions([]) + setGeneIds([]) + } + } + + const debounceFn = React.useCallback(debounce(onSearchChange, 500), []) + const gridsize = props.gridsize || 5.5 + return ( + + {props.showTitle && ( + + Search gene: +
    +     + )} + + { + if (event.key === "Enter") { + event.defaultPrevented = true + + value && + props.onSelected && + props.onSelected({ + geneid: geneids.find((g) => g.name === value)?.id.split(".")[0], + chromosome: geneids.find((g) => g.name === value)?.chrom, + start: geneids.find((g) => g.name === value)?.start, + end: geneids.find((g) => g.name === value)?.end, + }) + if (value) { + let chrom = geneids.find((g) => g.name === value)?.chrom + let start = geneids.find((g) => g.name === value)?.start + let end = geneids.find((g) => g.name === value)?.end + router.push(`search?assembly=${props.assembly}&chromosome=${chrom}&start=${start}&end=${end}&gene=${value}`) + } + } + }} + value={value} + onChange={(_: any, newValue: string | null) => { + setValue(newValue) + }} + inputValue={inputValue} + onInputChange={(event, newInputValue) => { + if (newInputValue != "") { + debounceFn(newInputValue) + } + + setInputValue(newInputValue) + }} + noOptionsText="e.g sox4,gapdh" + renderInput={(params) => ( + + )} + renderOption={(props, option) => { + return ( +
  • + + + + {option} + + {geneDesc && geneDesc.find((g) => g.name === option) && ( + + {geneDesc.find((g) => g.name === option)?.desc} + + )} + + +
    • + ) + }} + /> +     +     + ) +} diff --git a/screen2.0/src/common/components/mainsearch/MainSearch.tsx b/screen2.0/src/common/components/mainsearch/MainSearch.tsx new file mode 100644 index 00000000..8c9fc8e1 --- /dev/null +++ b/screen2.0/src/common/components/mainsearch/MainSearch.tsx @@ -0,0 +1,123 @@ +"use client" +import React, { useState } from "react" +import Grid2 from "../../mui-client-wrappers/Grid2" +import { Stack, TextField, IconButton, InputAdornment, InputBaseProps, createTheme } from "@mui/material" +import SearchIcon from "@mui/icons-material/Search" +import GenomeSwitch from "../GenomeSwitch" +import { useRouter } from "next/navigation" +import MenuItem from "@mui/material/MenuItem" +import FormControl from "@mui/material/FormControl" +import Select, { SelectChangeEvent } from "@mui/material/Select" +import { CcreAutoComplete } from "./CcreAutocomplete" +import { GeneAutoComplete } from "./GeneAutocomplete" +import { SnpAutoComplete } from "./SnpAutocomplete" +import { CelltypeAutocomplete } from "./CelltypeAutocomplete" + +export type MainSearchProps = InputBaseProps & { + //false for human, true for mouse + initialChecked?: boolean, + textColor?: string +} +const MainSearch: React.FC = (props: MainSearchProps) => { + const [value, setValue] = useState("") + const [checked, setChecked] = useState(props.initialChecked || false) + const [selectedSearch, setSelectedSearch] = useState("Genomic Region") + const assembly = checked ? "mm10" : "GRCh38" + const handleSearchChange = (event: SelectChangeEvent) => { + setSelectedSearch(event.target.value) + } + const router = useRouter() + + const handleChange = (event: { target: { value: React.SetStateAction } }) => { + setValue(event.target.value) + } + + function handleSubmit() { + const assembly = checked ? "mm10" : "GRCh38" + //if submitted with empty value, use default search + if (value == "") { + router.push(`/search?assembly=${assembly}&chromosome=chr11&start=5205263&end=5381894`) + return + } + const input = value.split(":") + const chromosome = input[0] + const coordinates = input[1].split("-") + const start = coordinates[0] + const end = coordinates[1] + router.push(`/search?assembly=${assembly}&chromosome=${chromosome}&start=${start}&end=${end}`) + } + + return ( + + + + + + + + + {selectedSearch === "Genomic Region" ? ( + { + if (event.code === "Enter") { + handleSubmit() + } + }} + InputProps={{ + endAdornment: ( + + handleSubmit()} sx={{ color: props.textColor || "black" }}> + + + + ), + style: { color: props.textColor || "black" }, + }} + sx={{ mr: "1em", ml: "1em", fieldset: { borderColor: props.textColor || "black" } }} + /> + ) : selectedSearch === "Gene Name" ? ( + + ) : selectedSearch === "SNP rsID" ? ( + + ) : selectedSearch === "Cell Type" ? ( + + ) : ( + + )} + + + setChecked(checked)} + /> + + + + ) +} + +export default MainSearch diff --git a/screen2.0/src/common/components/SnpAutocomplete.tsx b/screen2.0/src/common/components/mainsearch/SnpAutocomplete.tsx similarity index 52% rename from screen2.0/src/common/components/SnpAutocomplete.tsx rename to screen2.0/src/common/components/mainsearch/SnpAutocomplete.tsx index bbb47ded..8a5f715d 100644 --- a/screen2.0/src/common/components/SnpAutocomplete.tsx +++ b/screen2.0/src/common/components/mainsearch/SnpAutocomplete.tsx @@ -1,133 +1,152 @@ -import * as React from "react"; -import Box from "@mui/material/Box"; -import TextField from "@mui/material/TextField"; -import Autocomplete from "@mui/material/Autocomplete"; -import Grid from "@mui/material/Grid"; -import Typography from "@mui/material/Typography"; -import { debounce } from "@mui/material/utils"; -import { useRouter } from "next/navigation" - -const SNP_AUTOCOMPLETE_QUERY = ` -query snpAutocompleteQuery($snpid: String!, $assembly: String!) { - snpAutocompleteQuery(snpid: $snpid, assembly: $assembly) { - id - coordinates { - chromosome - start - end - } - } -} -`; -export const SnpAutoComplete = (props) => { - const [value, setValue] = React.useState(null); - const [inputValue, setInputValue] = React.useState(""); - const [options, setOptions] = React.useState([]); - const [snpids, setSnpIds] = React.useState([]); - const router = useRouter() - - const onSearchChange = async (value: any) => { - setOptions([]); - const response = await fetch("https://ga.staging.wenglab.org/graphql", { - method: "POST", - body: JSON.stringify({ - query: SNP_AUTOCOMPLETE_QUERY, - variables: { - assembly: "grch38", - snpid: value, - }, - }), - headers: { "Content-Type": "application/json" }, - }); - const snpSuggestion = (await response.json()).data?.snpAutocompleteQuery; - if (snpSuggestion && snpSuggestion.length > 0) { - const r = snpSuggestion.map((g: any) => g.id); - const snp = snpSuggestion.map((g: any) => { - return { - chrom: g.coordinates.chromosome, - start: g.coordinates.start, - end: g.coordinates.end, - id: g.id, - }; - }); - setOptions(r); - setSnpIds(snp); - } else if (snpSuggestion && snpSuggestion.length === 0) { - setOptions([]); - setSnpIds([]); - } - //setgeneCards([]); - }; - - const debounceFn = React.useCallback(debounce(onSearchChange, 500), []); - - return ( - - - { - if (event.key === "Enter") { - event.defaultPrevented = true; - - if (value) { - - let chromosome = snpids.find((g) => g.id === value)?.chrom - let start= snpids.find((g) => g.id === value)?.start - 2000 - let end= snpids.find((g) => g.id === value)?.end + 2000 - router.push(`search?assembly=${props.assembly}&chromosome=${chromosome}&start=${Math.max(0,start)}&end=${end}&snpid=${value}`) - } - } - }} - value={value} - onChange={(_: any, newValue: string | null) => { - setValue(newValue); - }} - inputValue={inputValue} - onInputChange={(event, newInputValue) => { - if (newInputValue != "") { - debounceFn(newInputValue); - } - - setInputValue(newInputValue); - }} - noOptionsText="e.g. rs11669173" - renderInput={(params) => ( - - )} - renderOption={(props, option) => { - return ( -
  • - - - - {option} - - {snpids && snpids.find((g) => g.id === option) && ( - - {`${snpids.find((g) => g.id === option)?.chrom}:${ - snpids.find((g) => g.id === option)?.start - }:${snpids.find((g) => g.id === option)?.end}`} - - )} - - -
    • - ); - }} - /> -     - -     - ); -}; +import * as React from "react" +import Box from "@mui/material/Box" +import TextField from "@mui/material/TextField" +import Autocomplete from "@mui/material/Autocomplete" +import Grid from "@mui/material/Grid" +import Typography from "@mui/material/Typography" +import { debounce } from "@mui/material/utils" +import { useRouter } from "next/navigation" + +const SNP_AUTOCOMPLETE_QUERY = ` +query snpAutocompleteQuery($snpid: String!, $assembly: String!) { + snpAutocompleteQuery(snpid: $snpid, assembly: $assembly) { + id + coordinates { + chromosome + start + end + } + } +} +` +export const SnpAutoComplete = (props) => { + const [value, setValue] = React.useState(null) + const [inputValue, setInputValue] = React.useState("") + const [options, setOptions] = React.useState([]) + const [snpids, setSnpIds] = React.useState([]) + const router = useRouter() + + const onSearchChange = async (value: any) => { + setOptions([]) + const response = await fetch("https://ga.staging.wenglab.org/graphql", { + method: "POST", + body: JSON.stringify({ + query: SNP_AUTOCOMPLETE_QUERY, + variables: { + assembly: "grch38", + snpid: value, + }, + }), + headers: { "Content-Type": "application/json" }, + }) + const snpSuggestion = (await response.json()).data?.snpAutocompleteQuery + if (snpSuggestion && snpSuggestion.length > 0) { + const r = snpSuggestion.map((g: any) => g.id) + const snp = snpSuggestion.map((g: any) => { + return { + chrom: g.coordinates.chromosome, + start: g.coordinates.start, + end: g.coordinates.end, + id: g.id, + } + }) + setOptions(r) + setSnpIds(snp) + } else if (snpSuggestion && snpSuggestion.length === 0) { + setOptions([]) + setSnpIds([]) + } + //setgeneCards([]); + } + + const debounceFn = React.useCallback(debounce(onSearchChange, 500), []) + + return ( + + + { + if (event.key === "Enter") { + event.defaultPrevented = true + + if (value) { + let chromosome = snpids.find((g) => g.id === value)?.chrom + let start = snpids.find((g) => g.id === value)?.start - 2000 + let end = snpids.find((g) => g.id === value)?.end + 2000 + router.push( + `search?assembly=${props.assembly}&chromosome=${chromosome}&start=${Math.max(0, start)}&end=${end}&snpid=${value}` + ) + } + } + }} + value={value} + onChange={(_: any, newValue: string | null) => { + setValue(newValue) + }} + inputValue={inputValue} + onInputChange={(event, newInputValue) => { + if (newInputValue != "") { + debounceFn(newInputValue) + } + + setInputValue(newInputValue) + }} + noOptionsText="e.g. rs11669173" + renderInput={(params) => ( + + )} + renderOption={(props, option) => { + return ( +
  • + + + + {option} + + {snpids && snpids.find((g) => g.id === option) && ( + + {`${snpids.find((g) => g.id === option)?.chrom}:${snpids.find((g) => g.id === option)?.start}:${ + snpids.find((g) => g.id === option)?.end + }`} + + )} + + +
    • + ) + }} + /> +     +     + ) +} diff --git a/screen2.0/yarn.lock b/screen2.0/yarn.lock index 867784be..1358687a 100644 --- a/screen2.0/yarn.lock +++ b/screen2.0/yarn.lock @@ -78,7 +78,7 @@ resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.22.10.tgz#e37634f9a12a1716136c44624ef54283cabd3f55" integrity sha512-lNbdGsQb9ekfsnjFGhEiF4hfFqGgfOP3H3d27re3n+CGhNuTSUEQdfWk556sTLNTloczcdM5TYF2LhzmDQKyvQ== -"@babel/runtime@^7.12.5", "@babel/runtime@^7.18.3", "@babel/runtime@^7.20.7", "@babel/runtime@^7.21.0", "@babel/runtime@^7.22.6", "@babel/runtime@^7.5.5", "@babel/runtime@^7.8.7": +"@babel/runtime@^7.12.5", "@babel/runtime@^7.18.3", "@babel/runtime@^7.20.7", "@babel/runtime@^7.21.0", "@babel/runtime@^7.22.6", "@babel/runtime@^7.3.1", "@babel/runtime@^7.5.5", "@babel/runtime@^7.8.3", "@babel/runtime@^7.8.7": version "7.22.10" resolved "https://registry.yarnpkg.com/@babel/runtime/-/runtime-7.22.10.tgz#ae3e9631fd947cb7e3610d3e9d8fef5f76696682" integrity sha512-21t/fkKLMZI4pqP2wlmsQAWnYW1PDyKyyUV4vCi+B25ydmdaYTKXPwCj0BzSUnZf4seIiYvSA3jcZ3gdsMFkLQ== @@ -360,6 +360,15 @@ "@mui/utils" "^5.14.4" prop-types "^15.8.1" +"@mui/private-theming@^5.14.5": + version "5.14.5" + resolved "https://registry.yarnpkg.com/@mui/private-theming/-/private-theming-5.14.5.tgz#834e1569c31e2644665f98d902def79014053017" + integrity sha512-cC4C5RrpXpDaaZyH9QwmPhRLgz+f2SYbOty3cPkk4qPSOSfif2ZEcDD9HTENKDDd9deB+xkPKzzZhi8cxIx8Ig== + dependencies: + "@babel/runtime" "^7.22.6" + "@mui/utils" "^5.14.5" + prop-types "^15.8.1" + "@mui/styled-engine@^5.13.2": version "5.13.2" resolved "https://registry.yarnpkg.com/@mui/styled-engine/-/styled-engine-5.13.2.tgz#c87bd61c0ab8086d34828b6defe97c02bcd642ef" @@ -370,6 +379,29 @@ csstype "^3.1.2" prop-types "^15.8.1" +"@mui/styles@^5.14.5": + version "5.14.5" + resolved "https://registry.yarnpkg.com/@mui/styles/-/styles-5.14.5.tgz#182759e844045b613a3c86266804642860c2fe53" + integrity sha512-yss4BRGae6ib4gq6YpVLnPyhHiuSIENwlDPWrTEqgc1UhTMmDBGZ7ZCdZ15YGdwviJuNDDf5Bcp3GK4rE5wZNQ== + dependencies: + "@babel/runtime" "^7.22.6" + "@emotion/hash" "^0.9.1" + "@mui/private-theming" "^5.14.5" + "@mui/types" "^7.2.4" + "@mui/utils" "^5.14.5" + clsx "^2.0.0" + csstype "^3.1.2" + hoist-non-react-statics "^3.3.2" + jss "^10.10.0" + jss-plugin-camel-case "^10.10.0" + jss-plugin-default-unit "^10.10.0" + jss-plugin-global "^10.10.0" + jss-plugin-nested "^10.10.0" + jss-plugin-props-sort "^10.10.0" + jss-plugin-rule-value-function "^10.10.0" + jss-plugin-vendor-prefixer "^10.10.0" + prop-types "^15.8.1" + "@mui/system@^5.14.4": version "5.14.4" resolved "https://registry.yarnpkg.com/@mui/system/-/system-5.14.4.tgz#306a2fdd41ab6f4912ea689316f834db8461bb86" @@ -400,6 +432,17 @@ prop-types "^15.8.1" react-is "^18.2.0" +"@mui/utils@^5.14.5": + version "5.14.5" + resolved "https://registry.yarnpkg.com/@mui/utils/-/utils-5.14.5.tgz#98fb6060610b793a8478e70ffe5e4ed5bd922dba" + integrity sha512-6Hzw63VR9C5xYv+CbjndoRLU6Gntal8rJ5W+GUzkyHrGWIyYPWZPa6AevnyGioySNETATe1H9oXS8f/7qgIHJA== + dependencies: + "@babel/runtime" "^7.22.6" + "@types/prop-types" "^15.7.5" + "@types/react-is" "^18.2.1" + prop-types "^15.8.1" + react-is "^18.2.0" + "@next/env@13.4.12": version "13.4.12" resolved "https://registry.yarnpkg.com/@next/env/-/env-13.4.12.tgz#0b88115ab817f178bf9dc0c5e7b367277595b58d" @@ -1595,6 +1638,14 @@ csrf@3.1.0: tsscmp "1.0.6" uid-safe "2.1.5" +css-vendor@^2.0.8: + version "2.0.8" + resolved "https://registry.yarnpkg.com/css-vendor/-/css-vendor-2.0.8.tgz#e47f91d3bd3117d49180a3c935e62e3d9f7f449d" + integrity sha512-x9Aq0XTInxrkuFeHKbYC7zWY8ai7qJ04Kxd9MnvbC1uO5DagxoHQjm4JvG+vCdXOoFtCjbL2XSZfxmoYa9uQVQ== + dependencies: + "@babel/runtime" "^7.8.3" + is-in-browser "^1.0.2" + cssesc@^3.0.0: version "3.0.0" resolved "https://registry.yarnpkg.com/cssesc/-/cssesc-3.0.0.tgz#37741919903b868565e1c09ea747445cd18983ee" @@ -2727,6 +2778,11 @@ human-signals@^4.3.0: resolved "https://registry.yarnpkg.com/human-signals/-/human-signals-4.3.1.tgz#ab7f811e851fca97ffbd2c1fe9a958964de321b2" integrity sha512-nZXjEF2nbo7lIw3mgYjItAfgQXog3OjJogSbKa2CQIIvSGWcKgeJnQlNXip6NglNzYH45nSRiEVimMvYL8DDqQ== +hyphenate-style-name@^1.0.3: + version "1.0.4" + resolved "https://registry.yarnpkg.com/hyphenate-style-name/-/hyphenate-style-name-1.0.4.tgz#691879af8e220aea5750e8827db4ef62a54e361d" + integrity sha512-ygGZLjmXfPHj+ZWh6LwbC37l43MhfztxetbFCoYTM2VjkIUpeHgSNn7QIyVFj7YQ1Wl9Cbw5sholVJPzWvC2MQ== + iconv-lite@0.4.24: version "0.4.24" resolved "https://registry.yarnpkg.com/iconv-lite/-/iconv-lite-0.4.24.tgz#2022b4b25fbddc21d2f524974a474aafe733908b" @@ -2922,6 +2978,11 @@ is-glob@^4.0.0, is-glob@^4.0.1, is-glob@^4.0.3, is-glob@~4.0.1: dependencies: is-extglob "^2.1.1" +is-in-browser@^1.0.2, is-in-browser@^1.1.3: + version "1.1.3" + resolved "https://registry.yarnpkg.com/is-in-browser/-/is-in-browser-1.1.3.tgz#56ff4db683a078c6082eb95dad7dc62e1d04f835" + integrity sha512-FeXIBgG/CPGd/WUxuEyvgGTEfwiG9Z4EKGxjNMRqviiIIfsmgrpnHLffEDdwUHqNva1VEW91o3xBT/m8Elgl9g== + is-negative-zero@^2.0.2: version "2.0.2" resolved "https://registry.yarnpkg.com/is-negative-zero/-/is-negative-zero-2.0.2.tgz#7bf6f03a28003b8b3965de3ac26f664d765f3150" @@ -3082,6 +3143,76 @@ json5@^2.1.2: resolved "https://registry.yarnpkg.com/json5/-/json5-2.2.3.tgz#78cd6f1a19bdc12b73db5ad0c61efd66c1e29283" integrity sha512-XmOWe7eyHYH14cLdVPoyg+GOH3rYX++KpzrylJwSW98t3Nk+U8XOl8FWKOgwtzdb8lXGf6zYwDUzeHMWfxasyg== +jss-plugin-camel-case@^10.10.0: + version "10.10.0" + resolved "https://registry.yarnpkg.com/jss-plugin-camel-case/-/jss-plugin-camel-case-10.10.0.tgz#27ea159bab67eb4837fa0260204eb7925d4daa1c" + integrity sha512-z+HETfj5IYgFxh1wJnUAU8jByI48ED+v0fuTuhKrPR+pRBYS2EDwbusU8aFOpCdYhtRc9zhN+PJ7iNE8pAWyPw== + dependencies: + "@babel/runtime" "^7.3.1" + hyphenate-style-name "^1.0.3" + jss "10.10.0" + +jss-plugin-default-unit@^10.10.0: + version "10.10.0" + resolved "https://registry.yarnpkg.com/jss-plugin-default-unit/-/jss-plugin-default-unit-10.10.0.tgz#db3925cf6a07f8e1dd459549d9c8aadff9804293" + integrity sha512-SvpajxIECi4JDUbGLefvNckmI+c2VWmP43qnEy/0eiwzRUsafg5DVSIWSzZe4d2vFX1u9nRDP46WCFV/PXVBGQ== + dependencies: + "@babel/runtime" "^7.3.1" + jss "10.10.0" + +jss-plugin-global@^10.10.0: + version "10.10.0" + resolved "https://registry.yarnpkg.com/jss-plugin-global/-/jss-plugin-global-10.10.0.tgz#1c55d3c35821fab67a538a38918292fc9c567efd" + integrity sha512-icXEYbMufiNuWfuazLeN+BNJO16Ge88OcXU5ZDC2vLqElmMybA31Wi7lZ3lf+vgufRocvPj8443irhYRgWxP+A== + dependencies: + "@babel/runtime" "^7.3.1" + jss "10.10.0" + +jss-plugin-nested@^10.10.0: + version "10.10.0" + resolved "https://registry.yarnpkg.com/jss-plugin-nested/-/jss-plugin-nested-10.10.0.tgz#db872ed8925688806e77f1fc87f6e62264513219" + integrity sha512-9R4JHxxGgiZhurDo3q7LdIiDEgtA1bTGzAbhSPyIOWb7ZubrjQe8acwhEQ6OEKydzpl8XHMtTnEwHXCARLYqYA== + dependencies: + "@babel/runtime" "^7.3.1" + jss "10.10.0" + tiny-warning "^1.0.2" + +jss-plugin-props-sort@^10.10.0: + version "10.10.0" + resolved "https://registry.yarnpkg.com/jss-plugin-props-sort/-/jss-plugin-props-sort-10.10.0.tgz#67f4dd4c70830c126f4ec49b4b37ccddb680a5d7" + integrity sha512-5VNJvQJbnq/vRfje6uZLe/FyaOpzP/IH1LP+0fr88QamVrGJa0hpRRyAa0ea4U/3LcorJfBFVyC4yN2QC73lJg== + dependencies: + "@babel/runtime" "^7.3.1" + jss "10.10.0" + +jss-plugin-rule-value-function@^10.10.0: + version "10.10.0" + resolved "https://registry.yarnpkg.com/jss-plugin-rule-value-function/-/jss-plugin-rule-value-function-10.10.0.tgz#7d99e3229e78a3712f78ba50ab342e881d26a24b" + integrity sha512-uEFJFgaCtkXeIPgki8ICw3Y7VMkL9GEan6SqmT9tqpwM+/t+hxfMUdU4wQ0MtOiMNWhwnckBV0IebrKcZM9C0g== + dependencies: + "@babel/runtime" "^7.3.1" + jss "10.10.0" + tiny-warning "^1.0.2" + +jss-plugin-vendor-prefixer@^10.10.0: + version "10.10.0" + resolved "https://registry.yarnpkg.com/jss-plugin-vendor-prefixer/-/jss-plugin-vendor-prefixer-10.10.0.tgz#c01428ef5a89f2b128ec0af87a314d0c767931c7" + integrity sha512-UY/41WumgjW8r1qMCO8l1ARg7NHnfRVWRhZ2E2m0DMYsr2DD91qIXLyNhiX83hHswR7Wm4D+oDYNC1zWCJWtqg== + dependencies: + "@babel/runtime" "^7.3.1" + css-vendor "^2.0.8" + jss "10.10.0" + +jss@10.10.0, jss@^10.10.0: + version "10.10.0" + resolved "https://registry.yarnpkg.com/jss/-/jss-10.10.0.tgz#a75cc85b0108c7ac8c7b7d296c520a3e4fbc6ccc" + integrity sha512-cqsOTS7jqPsPMjtKYDUpdFC0AbhYFLTcuGRqymgmdJIeQ8cH7+AgX7YSgQy79wXloZq2VvATYxUOUQEvS1V/Zw== + dependencies: + "@babel/runtime" "^7.3.1" + csstype "^3.0.2" + is-in-browser "^1.1.3" + tiny-warning "^1.0.2" + jstransformer@1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/jstransformer/-/jstransformer-1.0.0.tgz#ed8bf0921e2f3f1ed4d5c1a44f68709ed24722c3" @@ -4882,6 +5013,11 @@ through@^2.3.8: resolved "https://registry.yarnpkg.com/through/-/through-2.3.8.tgz#0dd4c9ffaabc357960b1b724115d7e0e86a2e1f5" integrity sha512-w89qg7PI8wAdvX60bMDP+bFoD5Dvhm9oLheFp5O4a2QF0cSBGsBX4qZmadPMvVqlLJBBci+WqGGOAPvcDeNSVg== +tiny-warning@^1.0.2: + version "1.0.3" + resolved "https://registry.yarnpkg.com/tiny-warning/-/tiny-warning-1.0.3.tgz#94a30db453df4c643d0fd566060d60a875d84754" + integrity sha512-lBN9zLN/oAf68o3zNXYrdCt1kP8WsiGW8Oo2ka41b2IM5JL/S1CTyX1rW0mb/zSuJun0ZUrDxx4sqvYS2FWzPA== + to-fast-properties@^2.0.0: version "2.0.0" resolved "https://registry.yarnpkg.com/to-fast-properties/-/to-fast-properties-2.0.0.tgz#dc5e698cbd079265bc73e0377681a4e4e83f616e" From efe0582ffdffabe57baa95d2c0df1aec7b970d99 Mon Sep 17 00:00:00 2001 From: NishiPhalke Date: Mon, 28 Aug 2023 18:09:36 -0400 Subject: [PATCH 3/8] reverting navbar search --- screen2.0/src/common/components/ResponsiveAppBar.tsx | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/screen2.0/src/common/components/ResponsiveAppBar.tsx b/screen2.0/src/common/components/ResponsiveAppBar.tsx index c5c88151..8681ae11 100644 --- a/screen2.0/src/common/components/ResponsiveAppBar.tsx +++ b/screen2.0/src/common/components/ResponsiveAppBar.tsx @@ -13,6 +13,7 @@ import nextConfig from "../../../next.config" import screenIcon from "../../../public/screenIcon.png" import { defaultTheme } from "../lib/themes" import MainSearch from "./mainsearch/MainSearch" +import HeaderSearch from "./HeaderSearch" // CLICKING ON LINKS ONCE THE POPUP IS OPEN IS BROKEN!!! @@ -247,9 +248,11 @@ function ResponsiveAppBar() { ))}     {/* TODO onSubmit for search box */} + - + + {/* Settings */} Date: Wed, 6 Sep 2023 10:46:13 -0400 Subject: [PATCH 4/8] refactoring --- .../mainsearch/CcreAutocomplete.tsx | 24 +++++++++---------- .../mainsearch/CelltypeAutocomplete.tsx | 21 ++++++---------- .../mainsearch/GeneAutocomplete.tsx | 6 ++--- .../components/mainsearch/SnpAutocomplete.tsx | 21 ++++++++-------- 4 files changed, 31 insertions(+), 41 deletions(-) diff --git a/screen2.0/src/common/components/mainsearch/CcreAutocomplete.tsx b/screen2.0/src/common/components/mainsearch/CcreAutocomplete.tsx index 19e6da50..25dfe285 100644 --- a/screen2.0/src/common/components/mainsearch/CcreAutocomplete.tsx +++ b/screen2.0/src/common/components/mainsearch/CcreAutocomplete.tsx @@ -29,7 +29,7 @@ export const CcreAutoComplete = (props) => { const [ccreAccessions, setCcreAccessions] = React.useState([]) const router = useRouter() - const onSearchChange = async (value: any) => { + const onSearchChange = async (value: string) => { setOptions([]) const response = await fetch("https://factorbook.api.wenglab.org/graphql", { method: "POST", @@ -45,8 +45,8 @@ export const CcreAutoComplete = (props) => { }) const ccreSuggestion = (await response.json()).data?.cCREQuery if (ccreSuggestion && ccreSuggestion.length > 0) { - const r = ccreSuggestion.map((g: any) => g.accession) - const ccres = ccreSuggestion.map((g: any) => { + const r = ccreSuggestion.map((g: { accession: string}) => g.accession) + const ccres = ccreSuggestion.map((g: { accession: string, coordinates: { start: number, end: number, chromosome: string }}) => { return { chrom: g.coordinates.chromosome, start: g.coordinates.start, @@ -81,15 +81,15 @@ export const CcreAutoComplete = (props) => { event.defaultPrevented = true if (value) { - let chrom = (ccreAccessions.find((g: any) => g.ccreaccession === value) as any)?.chrom - let start = (ccreAccessions.find((g: any) => g.ccreaccession === value) as any)?.start - let end = (ccreAccessions.find((g: any) => g.ccreaccession === value) as any)?.end + let chrom = (ccreAccessions.find((g: {ccreaccession: string}) => g.ccreaccession === value))?.chrom + let start = (ccreAccessions.find((g: {ccreaccession: string}) => g.ccreaccession === value))?.start + let end = (ccreAccessions.find((g: {ccreaccession: string}) => g.ccreaccession === value))?.end router.push(`search?assembly=${props.assembly}&chromosome=${chrom}&start=${start}&end=${end}&accession=${value}`) } } }} value={value} - onChange={(_: any, newValue: any) => { + onChange={(_, newValue: string | null) => { setValue(newValue) }} inputValue={inputValue} @@ -106,7 +106,7 @@ export const CcreAutoComplete = (props) => { {...params} label="Enter a cCRE accession" InputLabelProps={{ shrink: true, style: { color: props.textColor || "black" } }} - // InputProps={{ style: { color: props.textColor || "black" } }} + placeholder="e.g. EH38E0001314" fullWidth sx={{ fieldset: { borderColor: props.textColor || "black"}, '& .MuiInput-underline:after': { @@ -134,11 +134,11 @@ export const CcreAutoComplete = (props) => { {option} - {ccreAccessions && ccreAccessions.find((g: any) => g.ccreaccession === option) && ( + {ccreAccessions && ccreAccessions.find((g: {ccreaccession: string }) => g.ccreaccession === option) && ( - {`${(ccreAccessions.find((g: any) => g.ccreaccession === option) as any)?.chrom}:${ - (ccreAccessions.find((g: any) => g.ccreaccession === option) as any)?.start - }:${(ccreAccessions.find((g: any) => g.ccreaccession === option) as any)?.end}`} + {`${(ccreAccessions.find((g: {ccreaccession: string }) => g.ccreaccession === option))?.chrom}:${ + (ccreAccessions.find((g: {ccreaccession: string }) => g.ccreaccession === option))?.start + }:${(ccreAccessions.find((g: {ccreaccession: string }) => g.ccreaccession === option))?.end}`} )}     diff --git a/screen2.0/src/common/components/mainsearch/CelltypeAutocomplete.tsx b/screen2.0/src/common/components/mainsearch/CelltypeAutocomplete.tsx index ba991f30..c1863f1a 100644 --- a/screen2.0/src/common/components/mainsearch/CelltypeAutocomplete.tsx +++ b/screen2.0/src/common/components/mainsearch/CelltypeAutocomplete.tsx @@ -9,10 +9,10 @@ import { useRouter } from "next/navigation" import { gql, useQuery } from "@apollo/client" export const CelltypeAutocomplete = (props) => { - const [value, setValue] = useState(null) + const [value, setValue] = useState(null) const [inputValue, setInputValue] = useState("") - const [options, setOptions] = useState([]) - const [cellTypes, setCelltypes] = useState([]) + const [options, setOptions] = useState([]) + const [cellTypes, setCelltypes] = useState([]) const [loading, setLoading] = useState(false) const router = useRouter() @@ -22,7 +22,7 @@ export const CelltypeAutocomplete = (props) => { return response.json() }) .then((data) => { - //setCellTypes(data) + let byCt = Object.keys(data.byCellType).map((ct) => { return { value: ct, @@ -35,8 +35,7 @@ export const CelltypeAutocomplete = (props) => { setLoading(false) }) .catch((error: Error) => { - // logging - // throw error + console.log(error) }) setLoading(true) }, [props.assembly]) @@ -56,7 +55,6 @@ export const CelltypeAutocomplete = (props) => { onKeyDown={(event) => { if (event.key === "Enter") { event.defaultPrevented = true - if (value) { let tissue = cellTypes.find((g) => g.biosample_summary === value)?.tissue let biosample = cellTypes.find((g) => g.biosample_summary === value)?.value @@ -74,15 +72,11 @@ export const CelltypeAutocomplete = (props) => { } }} value={value} - onChange={(_: any, newValue: string | null) => { + onChange={(_, newValue: string | null) => { setValue(newValue) }} inputValue={inputValue} onInputChange={(event, newInputValue) => { - if (newInputValue != "") { - //debounceFn(newInputValue); - } - setInputValue(newInputValue) }} noOptionsText="e.g. LNCAP" @@ -90,8 +84,7 @@ export const CelltypeAutocomplete = (props) => { { - const [value, setValue] = React.useState(null) + const [value, setValue] = React.useState(null) const [inputValue, setInputValue] = React.useState("") const [options, setOptions] = React.useState([]) const [geneids, setGeneIds] = React.useState<{ chrom: string; start: number; end: number; id: string; name: string }[]>([]) @@ -132,7 +130,7 @@ export const GeneAutoComplete = (props) => { } }} value={value} - onChange={(_: any, newValue: string | null) => { + onChange={(_, newValue: string | null) => { setValue(newValue) }} inputValue={inputValue} diff --git a/screen2.0/src/common/components/mainsearch/SnpAutocomplete.tsx b/screen2.0/src/common/components/mainsearch/SnpAutocomplete.tsx index 8a5f715d..9c84173a 100644 --- a/screen2.0/src/common/components/mainsearch/SnpAutocomplete.tsx +++ b/screen2.0/src/common/components/mainsearch/SnpAutocomplete.tsx @@ -20,13 +20,13 @@ query snpAutocompleteQuery($snpid: String!, $assembly: String!) { } ` export const SnpAutoComplete = (props) => { - const [value, setValue] = React.useState(null) + const [value, setValue] = React.useState(null) const [inputValue, setInputValue] = React.useState("") - const [options, setOptions] = React.useState([]) - const [snpids, setSnpIds] = React.useState([]) + const [options, setOptions] = React.useState([]) + const [snpids, setSnpIds] = React.useState([]) const router = useRouter() - const onSearchChange = async (value: any) => { + const onSearchChange = async (value: string) => { setOptions([]) const response = await fetch("https://ga.staging.wenglab.org/graphql", { method: "POST", @@ -41,8 +41,8 @@ export const SnpAutoComplete = (props) => { }) const snpSuggestion = (await response.json()).data?.snpAutocompleteQuery if (snpSuggestion && snpSuggestion.length > 0) { - const r = snpSuggestion.map((g: any) => g.id) - const snp = snpSuggestion.map((g: any) => { + const r = snpSuggestion.map((g: {id: string}) => g.id) + const snp = snpSuggestion.map((g: {id: string, coordinates: {chromosome:string, start: number, end: number} }) => { return { chrom: g.coordinates.chromosome, start: g.coordinates.start, @@ -56,7 +56,7 @@ export const SnpAutoComplete = (props) => { setOptions([]) setSnpIds([]) } - //setgeneCards([]); + } const debounceFn = React.useCallback(debounce(onSearchChange, 500), []) @@ -88,11 +88,11 @@ export const SnpAutoComplete = (props) => { } }} value={value} - onChange={(_: any, newValue: string | null) => { + onChange={(_, newValue: string | null) => { setValue(newValue) }} inputValue={inputValue} - onInputChange={(event, newInputValue) => { + onInputChange={(_, newInputValue) => { if (newInputValue != "") { debounceFn(newInputValue) } @@ -104,8 +104,7 @@ export const SnpAutoComplete = (props) => { Date: Wed, 6 Sep 2023 10:56:46 -0400 Subject: [PATCH 5/8] refactoring --- .../src/app/search/gbview/defaulttracks.tsx | 2 +- screen2.0/src/app/search/gbview/tfmotiftrack.tsx | 4 ++-- .../src/common/components/MainResultsTable.tsx | 2 +- .../components/mainsearch/CcreAutocomplete.tsx | 12 ++++++------ .../mainsearch/CelltypeAutocomplete.tsx | 2 +- .../components/mainsearch/GeneAutocomplete.tsx | 16 ++++++++-------- 6 files changed, 19 insertions(+), 19 deletions(-) diff --git a/screen2.0/src/app/search/gbview/defaulttracks.tsx b/screen2.0/src/app/search/gbview/defaulttracks.tsx index 184b8b84..45e0a5d9 100644 --- a/screen2.0/src/app/search/gbview/defaulttracks.tsx +++ b/screen2.0/src/app/search/gbview/defaulttracks.tsx @@ -157,7 +157,7 @@ const DefaultTracks: React.FC = (props) => { () => associateBy( (data && data.bigRequests && data.bigRequests[0].data) || [], - (x: any) => x.name, + (x: { name: string}) => x.name, (x: any) => ({ chromosome: x.chr, start: x.start, end: x.end }) ), [data] diff --git a/screen2.0/src/app/search/gbview/tfmotiftrack.tsx b/screen2.0/src/app/search/gbview/tfmotiftrack.tsx index 90b3fcec..f086dacc 100644 --- a/screen2.0/src/app/search/gbview/tfmotiftrack.tsx +++ b/screen2.0/src/app/search/gbview/tfmotiftrack.tsx @@ -40,11 +40,11 @@ export const TfMotifTrack = (props) => { data={props.data} transform="translate(0,40)" tooltipContent={(rect: any) => { - console.log(rect, ":recg") + return }} onClick={(x: any) => { - //return window.open(`${x}`) + return window.open( `https://factorbook.org/tf/${props.assembly === "GRCh38" ? "human" : "mouse"}/${x.rectname.split("$")[2]}/motif`, "_blank" diff --git a/screen2.0/src/common/components/MainResultsTable.tsx b/screen2.0/src/common/components/MainResultsTable.tsx index 80f6234a..cf94e1b4 100644 --- a/screen2.0/src/common/components/MainResultsTable.tsx +++ b/screen2.0/src/common/components/MainResultsTable.tsx @@ -35,7 +35,7 @@ function MainResultsTable(props: Partial>) { }, { header: "Chr", - value: (row: { chromosome: any }) => row.chromosome, + value: (row: { chromosome: string }) => row.chromosome, }, { header: "Start", diff --git a/screen2.0/src/common/components/mainsearch/CcreAutocomplete.tsx b/screen2.0/src/common/components/mainsearch/CcreAutocomplete.tsx index 25dfe285..fac68e68 100644 --- a/screen2.0/src/common/components/mainsearch/CcreAutocomplete.tsx +++ b/screen2.0/src/common/components/mainsearch/CcreAutocomplete.tsx @@ -1,5 +1,5 @@ "use client" -import * as React from "react" +import React, {useState, useCallback} from "react" import Box from "@mui/material/Box" import TextField from "@mui/material/TextField" import Autocomplete from "@mui/material/Autocomplete" @@ -23,10 +23,10 @@ query cCREQuery($accession_prefix: [String!], $limit: Int, $assembly: String!) { } ` export const CcreAutoComplete = (props) => { - const [value, setValue] = React.useState(null) - const [inputValue, setInputValue] = React.useState("") - const [options, setOptions] = React.useState([]) - const [ccreAccessions, setCcreAccessions] = React.useState([]) + const [value, setValue] = useState(null) + const [inputValue, setInputValue] = useState("") + const [options, setOptions] = useState([]) + const [ccreAccessions, setCcreAccessions] = useState([]) const router = useRouter() const onSearchChange = async (value: string) => { @@ -62,7 +62,7 @@ export const CcreAutoComplete = (props) => { } } - const debounceFn = React.useCallback(debounce(onSearchChange, 500), []) + const debounceFn = useCallback(debounce(onSearchChange, 500), []) return ( diff --git a/screen2.0/src/common/components/mainsearch/CelltypeAutocomplete.tsx b/screen2.0/src/common/components/mainsearch/CelltypeAutocomplete.tsx index c1863f1a..cfd68628 100644 --- a/screen2.0/src/common/components/mainsearch/CelltypeAutocomplete.tsx +++ b/screen2.0/src/common/components/mainsearch/CelltypeAutocomplete.tsx @@ -1,4 +1,4 @@ -import React, { useMemo, useState, useRef, useCallback, useEffect } from "react" +import React, { useState, useEffect } from "react" import Box from "@mui/material/Box" import TextField from "@mui/material/TextField" import Autocomplete from "@mui/material/Autocomplete" diff --git a/screen2.0/src/common/components/mainsearch/GeneAutocomplete.tsx b/screen2.0/src/common/components/mainsearch/GeneAutocomplete.tsx index 18aa7301..1219bacf 100644 --- a/screen2.0/src/common/components/mainsearch/GeneAutocomplete.tsx +++ b/screen2.0/src/common/components/mainsearch/GeneAutocomplete.tsx @@ -1,4 +1,4 @@ -import * as React from "react" +import React, { useState, useEffect, useCallback } from "react" import Box from "@mui/material/Box" import TextField from "@mui/material/TextField" import Autocomplete from "@mui/material/Autocomplete" @@ -23,15 +23,15 @@ query ($assembly: String!, $name_prefix: [String!], $limit: Int) { ` export const GeneAutoComplete = (props) => { - const [value, setValue] = React.useState(null) - const [inputValue, setInputValue] = React.useState("") - const [options, setOptions] = React.useState([]) - const [geneids, setGeneIds] = React.useState<{ chrom: string; start: number; end: number; id: string; name: string }[]>([]) + const [value, setValue] = useState(null) + const [inputValue, setInputValue] = useState("") + const [options, setOptions] = useState([]) + const [geneids, setGeneIds] = useState<{ chrom: string; start: number; end: number; id: string; name: string }[]>([]) const router = useRouter() - const [geneDesc, setgeneDesc] = React.useState<{ name: string; desc: string }[]>() + const [geneDesc, setgeneDesc] = useState<{ name: string; desc: string }[]>() - React.useEffect(() => { + useEffect(() => { const fetchData = async () => { let f = await Promise.all( options.map((gene) => @@ -89,7 +89,7 @@ export const GeneAutoComplete = (props) => { } } - const debounceFn = React.useCallback(debounce(onSearchChange, 500), []) + const debounceFn = useCallback(debounce(onSearchChange, 500), []) const gridsize = props.gridsize || 5.5 return ( From b1a83bcb0fbd131bd22d2f2fe944832f59c5e3fc Mon Sep 17 00:00:00 2001 From: NishiPhalke Date: Wed, 6 Sep 2023 11:03:33 -0400 Subject: [PATCH 6/8] refactoring --- screen2.0/src/app/search/ccresearch.tsx | 7 ++++--- screen2.0/src/app/search/gbview/defaulttracks.tsx | 1 + 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/screen2.0/src/app/search/ccresearch.tsx b/screen2.0/src/app/search/ccresearch.tsx index d24e9f4c..0d99ff20 100644 --- a/screen2.0/src/app/search/ccresearch.tsx +++ b/screen2.0/src/app/search/ccresearch.tsx @@ -47,10 +47,11 @@ export const CcreSearch = (props: { mainQueryParams, ccrerows: MainResultTableRo setTabIndex(val)}> - + + - {tabIndex === 0 && ( + {tabIndex === 1 && ( )} - {tabIndex === 1 && ( + {tabIndex === 0 && ( = (props) => {     {(data?.bigRequests || []).map((data, i) => ( Date: Wed, 6 Sep 2023 11:19:34 -0400 Subject: [PATCH 7/8] refactoring --- screen2.0/src/app/search/gbview/biosampletracks.tsx | 1 + screen2.0/src/app/search/gbview/genomebrowserview.tsx | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/screen2.0/src/app/search/gbview/biosampletracks.tsx b/screen2.0/src/app/search/gbview/biosampletracks.tsx index 27342eed..791c444b 100644 --- a/screen2.0/src/app/search/gbview/biosampletracks.tsx +++ b/screen2.0/src/app/search/gbview/biosampletracks.tsx @@ -137,6 +137,7 @@ export const BiosampleTracks: React.FC = (props) => {     {(data?.bigRequests || []).map((data, i) => ( = (props) => { ]) setTracks(tracks) } - }, [bdata, props.biosample]) + }, [bdata, props.biosample,props.assembly]) return ( <> From e70797dc57cc483247fd93ed06b4b4167dd421fa Mon Sep 17 00:00:00 2001 From: NishiPhalke Date: Wed, 6 Sep 2023 14:40:31 -0400 Subject: [PATCH 8/8] fixed review comments --- screen2.0/package.json | 3 +- .../gene-expression/gene-autocomplete.tsx | 4 +- .../src/app/search/ccredetails/client.ts | 3 +- .../src/app/search/gbview/biosampletracks.tsx | 52 +------- .../src/app/search/gbview/defaulttracks.tsx | 36 +----- screen2.0/src/app/search/gbview/queries.ts | 30 +++++ screen2.0/src/app/search/gbview/types.ts | 21 ++++ screen2.0/src/app/search/page.tsx | 1 - .../mainsearch/CcreAutocomplete.tsx | 24 +--- .../mainsearch/CelltypeAutocomplete.tsx | 28 ++--- .../mainsearch/GeneAutocomplete.tsx | 49 ++------ .../components/mainsearch/SnpAutocomplete.tsx | 20 +-- .../common/components/mainsearch/queries.ts | 41 ++++++ screen2.0/src/common/lib/client.ts | 4 +- screen2.0/src/common/lib/queries.ts | 5 +- screen2.0/src/config.json | 7 ++ screen2.0/yarn.lock | 118 +----------------- 17 files changed, 155 insertions(+), 291 deletions(-) create mode 100644 screen2.0/src/app/search/gbview/queries.ts create mode 100644 screen2.0/src/app/search/gbview/types.ts create mode 100644 screen2.0/src/common/components/mainsearch/queries.ts diff --git a/screen2.0/package.json b/screen2.0/package.json index a857f347..f5157a76 100644 --- a/screen2.0/package.json +++ b/screen2.0/package.json @@ -41,8 +41,7 @@ "@emotion/styled": "^11.11.0", "@mui/icons-material": "^5.14.3", "@mui/lab": "^5.0.0-alpha.137", - "@mui/material": "^5.14.2", - "@mui/styles": "^5.14.5", + "@mui/material": "^5.14.2", "@types/node": "^20.4.9", "@types/react": "^18.2.19", "@types/react-dom": "18.2.7", diff --git a/screen2.0/src/app/applets/gene-expression/gene-autocomplete.tsx b/screen2.0/src/app/applets/gene-expression/gene-autocomplete.tsx index d4fb225a..1187bc75 100644 --- a/screen2.0/src/app/applets/gene-expression/gene-autocomplete.tsx +++ b/screen2.0/src/app/applets/gene-expression/gene-autocomplete.tsx @@ -8,7 +8,7 @@ import Grid2 from "@mui/material/Unstable_Grid2/Grid2" import { gene } from "./types" import { QueryResponse } from "../../../../types/types" import { Dispatch, SetStateAction } from "react" - +import Config from "../../../config.json" const GENE_AUTOCOMPLETE_QUERY = ` query ($assembly: String!, $name_prefix: [String!], $limit: Int) { gene(assembly: $assembly, name_prefix: $name_prefix, limit: $limit) { @@ -66,7 +66,7 @@ export default function GeneAutoComplete(props: { // gene list const onSearchChange = async (value: string) => { setOptions([]) - const response = await fetch("https://ga.staging.wenglab.org/graphql", { + const response = await fetch(Config.API.GraphqlAPI, { method: "POST", body: JSON.stringify({ query: GENE_AUTOCOMPLETE_QUERY, diff --git a/screen2.0/src/app/search/ccredetails/client.ts b/screen2.0/src/app/search/ccredetails/client.ts index c70b4e8b..57600f08 100644 --- a/screen2.0/src/app/search/ccredetails/client.ts +++ b/screen2.0/src/app/search/ccredetails/client.ts @@ -1,5 +1,6 @@ import { ApolloClient, InMemoryCache } from "@apollo/client" +import Config from "../../../config.json" export const client = new ApolloClient({ - uri: "https://factorbook.api.wenglab.org/graphql", + uri: Config.API.CcreAPI, cache: new InMemoryCache(), }) diff --git a/screen2.0/src/app/search/gbview/biosampletracks.tsx b/screen2.0/src/app/search/gbview/biosampletracks.tsx index 791c444b..88e881e6 100644 --- a/screen2.0/src/app/search/gbview/biosampletracks.tsx +++ b/screen2.0/src/app/search/gbview/biosampletracks.tsx @@ -1,18 +1,13 @@ -import { gql, useQuery } from "@apollo/client" +import { useQuery } from "@apollo/client" import { associateBy } from "queryz" -import { BigWigData, BigBedData, BigZoomData } from "bigwig-reader" + import React, { RefObject, useEffect, useMemo, useState } from "react" import { EmptyTrack } from "umms-gb" -import { RequestError } from "umms-gb/dist/components/tracks/trackset/types" -import { ValuedPoint } from "umms-gb/dist/utils/types" import { client } from "../ccredetails/client" import { TitledTrack } from "./defaulttracks" +import { BIOSAMPLE_QUERY, BIG_QUERY } from "./queries" +import { GenomicRange, BigQueryResponse } from "./types" -type GenomicRange = { - chromosome?: string - start: number - end: number -} type BiosampleTracksProps = { tracks: [string, string, string][] @@ -29,28 +24,6 @@ type BiosampleTracksProps = { onSettingsClick?: () => void } -export type BigResponseData = BigWigData[] | BigBedData[] | BigZoomData[] | ValuedPoint[] - -export type BigResponse = { - data: BigResponseData - error: RequestError -} - -export type BigQueryResponse = { - bigRequests: BigResponse[] -} -export const BIG_QUERY = gql` - query BigRequests($bigRequests: [BigRequest!]!) { - bigRequests(requests: $bigRequests) { - data - error { - errortype - message - } - } - } -` - export const COLOR_MAP: Map = new Map([ ["DNase", "#06da93"], ["H3K4me3", "#ff0000"], @@ -58,23 +31,6 @@ export const COLOR_MAP: Map = new Map([ ["CTCF", "#00b0d0"], ]) -export const BIOSAMPLE_QUERY = gql` - query q($assembly: String!) { - ccREBiosampleQuery(assembly: $assembly) { - biosamples { - name - dnase: experimentAccession(assay: "DNase") - h3k4me3: experimentAccession(assay: "H3K4me3") - h3k27ac: experimentAccession(assay: "H3K27ac") - ctcf: experimentAccession(assay: "CTCF") - dnase_signal: fileAccession(assay: "DNase") - h3k4me3_signal: fileAccession(assay: "H3K4me3") - h3k27ac_signal: fileAccession(assay: "H3K27ac") - ctcf_signal: fileAccession(assay: "CTCF") - } - } - } -` export const BiosampleTracks: React.FC = (props) => { const [cTracks, setTracks] = useState<[string, string, string][]>(props.tracks) diff --git a/screen2.0/src/app/search/gbview/defaulttracks.tsx b/screen2.0/src/app/search/gbview/defaulttracks.tsx index 70140c70..972d147f 100644 --- a/screen2.0/src/app/search/gbview/defaulttracks.tsx +++ b/screen2.0/src/app/search/gbview/defaulttracks.tsx @@ -1,24 +1,13 @@ -import { gql, useQuery } from "@apollo/client" +import { useQuery } from "@apollo/client" import { associateBy } from "queryz" -import { BigWigData, BigBedData, BigZoomData } from "bigwig-reader" +import { BigWigData, BigBedData } from "bigwig-reader" import React, { RefObject, useEffect, useMemo, useState } from "react" import { DenseBigBed, EmptyTrack, FullBigWig } from "umms-gb" -import { RequestError } from "umms-gb/dist/components/tracks/trackset/types" -import { ValuedPoint } from "umms-gb/dist/utils/types" import { client } from "../ccredetails/client" import CCRETooltip from "./ccretooltip" +import { BIG_QUERY } from "./queries" +import { GenomicRange, BigQueryResponse, BigResponseData } from "./types" -export const BIG_QUERY = gql` - query BigRequests($bigRequests: [BigRequest!]!) { - bigRequests(requests: $bigRequests) { - data - error { - errortype - message - } - } - } -` export const COLOR_MAP: Map = new Map([ ["Aggregated DNase-seq signal, all Registry biosamples", "#06da93"], @@ -27,23 +16,6 @@ export const COLOR_MAP: Map = new Map([ ["Aggregated CTCF ChIP-seq signal, all Registry biosamples", "#00b0d0"], ]) -type GenomicRange = { - chromosome?: string - start: number - end: number -} - -export type BigResponseData = BigWigData[] | BigBedData[] | BigZoomData[] | ValuedPoint[] - -export type BigResponse = { - data: BigResponseData - error: RequestError -} - -export type BigQueryResponse = { - bigRequests: BigResponse[] -} - type DefaultTracksProps = { domain: GenomicRange onHeightChanged?: (i: number) => void diff --git a/screen2.0/src/app/search/gbview/queries.ts b/screen2.0/src/app/search/gbview/queries.ts new file mode 100644 index 00000000..46216dab --- /dev/null +++ b/screen2.0/src/app/search/gbview/queries.ts @@ -0,0 +1,30 @@ +import { gql } from "@apollo/client" +export const BIG_QUERY = gql` + query BigRequests($bigRequests: [BigRequest!]!) { + bigRequests(requests: $bigRequests) { + data + error { + errortype + message + } + } + } +` + +export const BIOSAMPLE_QUERY = gql` + query q($assembly: String!) { + ccREBiosampleQuery(assembly: $assembly) { + biosamples { + name + dnase: experimentAccession(assay: "DNase") + h3k4me3: experimentAccession(assay: "H3K4me3") + h3k27ac: experimentAccession(assay: "H3K27ac") + ctcf: experimentAccession(assay: "CTCF") + dnase_signal: fileAccession(assay: "DNase") + h3k4me3_signal: fileAccession(assay: "H3K4me3") + h3k27ac_signal: fileAccession(assay: "H3K27ac") + ctcf_signal: fileAccession(assay: "CTCF") + } + } + } +` diff --git a/screen2.0/src/app/search/gbview/types.ts b/screen2.0/src/app/search/gbview/types.ts new file mode 100644 index 00000000..983c2e16 --- /dev/null +++ b/screen2.0/src/app/search/gbview/types.ts @@ -0,0 +1,21 @@ +import { BigWigData, BigBedData, BigZoomData } from "bigwig-reader" +import { RequestError } from "umms-gb/dist/components/tracks/trackset/types" +import { ValuedPoint } from "umms-gb/dist/utils/types" + + +export type BigResponseData = BigWigData[] | BigBedData[] | BigZoomData[] | ValuedPoint[] + +export type BigResponse = { + data: BigResponseData + error: RequestError +} + +export type BigQueryResponse = { + bigRequests: BigResponse[] +} + +export type GenomicRange = { + chromosome?: string + start: number + end: number + } \ No newline at end of file diff --git a/screen2.0/src/app/search/page.tsx b/screen2.0/src/app/search/page.tsx index 860a2a0f..1ffb1c35 100644 --- a/screen2.0/src/app/search/page.tsx +++ b/screen2.0/src/app/search/page.tsx @@ -4,7 +4,6 @@ import { MainQuery, getGlobals, linkedGenesQuery } from "../../common/lib/querie import { ApolloQueryResult } from "@apollo/client" import { cCREData, CellTypeData, MainQueryParams, MainResultTableRow, MainResultTableRows } from "./types" import { checkTrueFalse, passesCriteria } from "../../common/lib/filter-helpers" -import { LinkedGenes } from "./ccredetails/linkedgenes" export default async function Search({ // Object from URL, see https://nextjs.org/docs/app/api-reference/file-conventions/page#searchparams-optional diff --git a/screen2.0/src/common/components/mainsearch/CcreAutocomplete.tsx b/screen2.0/src/common/components/mainsearch/CcreAutocomplete.tsx index fac68e68..c234e61c 100644 --- a/screen2.0/src/common/components/mainsearch/CcreAutocomplete.tsx +++ b/screen2.0/src/common/components/mainsearch/CcreAutocomplete.tsx @@ -7,22 +7,10 @@ import Grid from "@mui/material/Grid" import Typography from "@mui/material/Typography" import { debounce } from "@mui/material/utils" import { useRouter } from "next/navigation" +import { CCRE_AUTOCOMPLETE_QUERY } from "./queries" +import Config from "../../../config.json" -///search?assembly=GRCh38&chromosome=chr11&start=5205263&end=5381894&accession=EH38E1516972 - -const CCRE_AUTOCOMPLETE_QUERY = ` -query cCREQuery($accession_prefix: [String!], $limit: Int, $assembly: String!) { - cCREQuery(accession_prefix: $accession_prefix, assembly: $assembly, limit: $limit) { - accession - coordinates { - start - end - chromosome - } - } -} -` -export const CcreAutoComplete = (props) => { +export const CcreAutoComplete: React.FC<{assembly: string, textColor: string }> = (props) => { const [value, setValue] = useState(null) const [inputValue, setInputValue] = useState("") const [options, setOptions] = useState([]) @@ -31,14 +19,14 @@ export const CcreAutoComplete = (props) => { const router = useRouter() const onSearchChange = async (value: string) => { setOptions([]) - const response = await fetch("https://factorbook.api.wenglab.org/graphql", { + const response = await fetch(Config.API.CcreAPI, { method: "POST", body: JSON.stringify({ query: CCRE_AUTOCOMPLETE_QUERY, variables: { assembly: props.assembly, accession_prefix: [value], - limit: 100, + limit: 100 }, }), headers: { "Content-Type": "application/json" }, @@ -100,7 +88,7 @@ export const CcreAutoComplete = (props) => { setInputValue(newInputValue) }} - noOptionsText="e.g. EH38E0001314" + noOptionsText={props.assembly==="mm10"? "e.g EM10E0000207": "e.g. EH38E0001314"} renderInput={(params) => ( { +export const CelltypeAutocomplete: React.FC<{assembly: string, textColor: string }> = (props) => { const [value, setValue] = useState(null) const [inputValue, setInputValue] = useState("") const [options, setOptions] = useState([]) const [cellTypes, setCelltypes] = useState([]) - const [loading, setLoading] = useState(false) + const router = useRouter() - + useEffect(() => { - fetch("https://downloads.wenglab.org/databyct.json") + fetch(props.assembly.toLowerCase()==="grch38" ? Config.API.HumanGlobals : Config.API.MouseGlobals) .then((response) => { return response.json() }) - .then((data) => { - + .then((data) => { let byCt = Object.keys(data.byCellType).map((ct) => { return { value: ct, @@ -31,19 +29,19 @@ export const CelltypeAutocomplete = (props) => { } }) setOptions(byCt.map((ct) => ct.biosample_summary)) - setCelltypes(byCt) - setLoading(false) + setCelltypes(byCt) }) .catch((error: Error) => { console.log(error) }) - setLoading(true) + }, [props.assembly]) return ( { if (event.key === "Enter") { event.defaultPrevented = true if (value) { + console.log(value,"ct") let tissue = cellTypes.find((g) => g.biosample_summary === value)?.tissue let biosample = cellTypes.find((g) => g.biosample_summary === value)?.value let biosample_summary = value.split(":")[0] @@ -76,16 +75,17 @@ export const CelltypeAutocomplete = (props) => { setValue(newValue) }} inputValue={inputValue} - onInputChange={(event, newInputValue) => { + onInputChange={(_, newInputValue) => { + setValue(newInputValue) setInputValue(newInputValue) }} - noOptionsText="e.g. LNCAP" + noOptionsText={props.assembly==="mm10" ? "strain B6NCrl cortical plate tissue male adult (8 weeks)" :"e.g. LNCAP"} renderInput={(params) => ( { +export const GeneAutoComplete: React.FC<{assembly: string, textColor: string }> = (props) => { const [value, setValue] = useState(null) const [inputValue, setInputValue] = useState("") const [options, setOptions] = useState([]) @@ -57,14 +45,14 @@ export const GeneAutoComplete = (props) => { const onSearchChange = async (value: string) => { setOptions([]) - const response = await fetch("https://ga.staging.wenglab.org/graphql", { + const response = await fetch(Config.API.GraphqlAPI, { method: "POST", body: JSON.stringify({ query: GENE_AUTOCOMPLETE_QUERY, variables: { - assembly: "GRCh38", + assembly: props.assembly.toLowerCase(), name_prefix: value, - limit: 1000, + limit: 1000 }, }), headers: { "Content-Type": "application/json" }, @@ -90,15 +78,9 @@ export const GeneAutoComplete = (props) => { } const debounceFn = useCallback(debounce(onSearchChange, 500), []) - const gridsize = props.gridsize || 5.5 + const gridsize = 5.5 return ( - - {props.showTitle && ( - - Search gene: -
    -     - )} + { if (event.key === "Enter") { event.defaultPrevented = true - value && - props.onSelected && - props.onSelected({ - geneid: geneids.find((g) => g.name === value)?.id.split(".")[0], - chromosome: geneids.find((g) => g.name === value)?.chrom, - start: geneids.find((g) => g.name === value)?.start, - end: geneids.find((g) => g.name === value)?.end, - }) + if (value) { let chrom = geneids.find((g) => g.name === value)?.chrom let start = geneids.find((g) => g.name === value)?.start @@ -134,7 +109,7 @@ export const GeneAutoComplete = (props) => { setValue(newValue) }} inputValue={inputValue} - onInputChange={(event, newInputValue) => { + onInputChange={(_, newInputValue) => { if (newInputValue != "") { debounceFn(newInputValue) } @@ -148,7 +123,7 @@ export const GeneAutoComplete = (props) => { label="Enter a gene name" InputLabelProps={{ shrink: true, style: { color: props.textColor || "black" } }} - placeholder="e.g sox4,gapdh" + placeholder={props.assembly==="mm10" ? "e.g Scml2,Dbt" : "e.g sox4,gapdh"} fullWidth sx={{ fieldset: { borderColor: props.textColor || "black"}, '& .MuiInput-underline:after': { borderBottomColor: props.textColor || "black", diff --git a/screen2.0/src/common/components/mainsearch/SnpAutocomplete.tsx b/screen2.0/src/common/components/mainsearch/SnpAutocomplete.tsx index 9c84173a..37ca48e1 100644 --- a/screen2.0/src/common/components/mainsearch/SnpAutocomplete.tsx +++ b/screen2.0/src/common/components/mainsearch/SnpAutocomplete.tsx @@ -6,20 +6,10 @@ import Grid from "@mui/material/Grid" import Typography from "@mui/material/Typography" import { debounce } from "@mui/material/utils" import { useRouter } from "next/navigation" +import { SNP_AUTOCOMPLETE_QUERY } from "./queries" +import Config from "../../../config.json" -const SNP_AUTOCOMPLETE_QUERY = ` -query snpAutocompleteQuery($snpid: String!, $assembly: String!) { - snpAutocompleteQuery(snpid: $snpid, assembly: $assembly) { - id - coordinates { - chromosome - start - end - } - } -} -` -export const SnpAutoComplete = (props) => { +export const SnpAutoComplete: React.FC<{assembly: string, textColor: string }> = (props) => { const [value, setValue] = React.useState(null) const [inputValue, setInputValue] = React.useState("") const [options, setOptions] = React.useState([]) @@ -28,12 +18,12 @@ export const SnpAutoComplete = (props) => { const onSearchChange = async (value: string) => { setOptions([]) - const response = await fetch("https://ga.staging.wenglab.org/graphql", { + const response = await fetch(Config.API.GraphqlAPI, { method: "POST", body: JSON.stringify({ query: SNP_AUTOCOMPLETE_QUERY, variables: { - assembly: "grch38", + assembly: props.assembly.toLowerCase(), snpid: value, }, }), diff --git a/screen2.0/src/common/components/mainsearch/queries.ts b/screen2.0/src/common/components/mainsearch/queries.ts new file mode 100644 index 00000000..8b53216c --- /dev/null +++ b/screen2.0/src/common/components/mainsearch/queries.ts @@ -0,0 +1,41 @@ + +export const CCRE_AUTOCOMPLETE_QUERY = ` +query cCREQuery($accession_prefix: [String!], $limit: Int, $assembly: String!) { + cCREQuery(accession_prefix: $accession_prefix, assembly: $assembly, limit: $limit) { + accession + coordinates { + start + end + chromosome + } + } +} +` + + +export const GENE_AUTOCOMPLETE_QUERY = ` +query ($assembly: String!, $name_prefix: [String!], $limit: Int) { + gene(assembly: $assembly, name_prefix: $name_prefix, limit: $limit) { + name + id + coordinates { + start + chromosome + end + } + } + } + ` + + export const SNP_AUTOCOMPLETE_QUERY = ` + query snpAutocompleteQuery($snpid: String!, $assembly: String!) { + snpAutocompleteQuery(snpid: $snpid, assembly: $assembly) { + id + coordinates { + chromosome + start + end + } + } + } + ` \ No newline at end of file diff --git a/screen2.0/src/common/lib/client.ts b/screen2.0/src/common/lib/client.ts index 88aea77b..a97aeed7 100644 --- a/screen2.0/src/common/lib/client.ts +++ b/screen2.0/src/common/lib/client.ts @@ -1,6 +1,6 @@ import { ApolloClient, HttpLink, InMemoryCache } from "@apollo/client" import { registerApolloClient } from "@apollo/experimental-nextjs-app-support/rsc" - +import Config from "../../config.json" /** * @returns an ApolloClient instance scoped for the current request */ @@ -10,7 +10,7 @@ export const { getClient } = registerApolloClient(() => { ssrMode: true, cache: new InMemoryCache(), link: new HttpLink({ - uri: "https://factorbook.api.wenglab.org/graphql", + uri: Config.API.CcreAPI, // you can disable result caching here if you want to // (this does not work if you are rendering your page with `export const dynamic = "force-static"`) // fetchOptions: { cache: "no-store" }, diff --git a/screen2.0/src/common/lib/queries.ts b/screen2.0/src/common/lib/queries.ts index 31c354f8..7033e8ce 100644 --- a/screen2.0/src/common/lib/queries.ts +++ b/screen2.0/src/common/lib/queries.ts @@ -4,6 +4,7 @@ import { getClient } from "../lib/client" import { ApolloQueryResult, gql } from "@apollo/client" +import Config from "../../config.json" const cCRE_QUERY = gql` query ccreSearchQuery( @@ -426,9 +427,9 @@ export const getGlobals = async (assembly: "GRCh38" | "mm10") => { // console.log(assembly) let res: Response if (assembly === "GRCh38") { - res = await fetch("https://downloads.wenglab.org/databyct.json") + res = await fetch(Config.API.HumanGlobals) } else if (assembly === "mm10") { - res = await fetch("https://downloads.wenglab.org/mm10_byct.json") + res = await fetch(Config.API.MouseGlobals) } return res.json() } diff --git a/screen2.0/src/config.json b/screen2.0/src/config.json index e58e9f3c..30211a9a 100644 --- a/screen2.0/src/config.json +++ b/screen2.0/src/config.json @@ -30,7 +30,14 @@ "staticServer": "/assets", "overrides": {} }, + "API": { + "HumanGlobals": "https://downloads.wenglab.org/databyct.json", + "MouseGlobals": "https://downloads.wenglab.org/mm10_byct.json", + "CcreAPI": "https://factorbook.api.wenglab.org/graphql", + "GraphqlAPI": "https://ga.staging.wenglab.org/graphql" + }, "Downloads": { + "HumanCCREs": "https://downloads.wenglab.org/Registry-V4/GRCh38-cCREs.bed", "HumanPromoters": "https://downloads.wenglab.org/Registry-V4/GRCh38-cCREs.PLS.bed", "HumanProximalEnhancers": "https://downloads.wenglab.org/Registry-V4/GRCh38-cCREs.pELS.bed", diff --git a/screen2.0/yarn.lock b/screen2.0/yarn.lock index 9cc1c722..21fcc30f 100644 --- a/screen2.0/yarn.lock +++ b/screen2.0/yarn.lock @@ -78,7 +78,7 @@ resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.22.13.tgz#23fb17892b2be7afef94f573031c2f4b42839a2b" integrity sha512-3l6+4YOvc9wx7VlCSw4yQfcBo01ECA8TicQfbnCPuCEpRQrf+gTUyGdxNw+pyTUyywp6JRD1w0YQs9TpBXYlkw== -"@babel/runtime@^7.12.5", "@babel/runtime@^7.18.3", "@babel/runtime@^7.20.7", "@babel/runtime@^7.22.10", "@babel/runtime@^7.3.1", "@babel/runtime@^7.5.5", "@babel/runtime@^7.8.3", "@babel/runtime@^7.8.7": +"@babel/runtime@^7.12.5", "@babel/runtime@^7.18.3", "@babel/runtime@^7.20.7", "@babel/runtime@^7.22.10", "@babel/runtime@^7.5.5", "@babel/runtime@^7.8.7": version "7.22.11" resolved "https://registry.yarnpkg.com/@babel/runtime/-/runtime-7.22.11.tgz#7a9ba3bbe406ad6f9e8dd4da2ece453eb23a77a4" integrity sha512-ee7jVNlWN09+KftVOu9n7S8gQzD/Z6hN/I8VBRXW4P1+Xe7kJGXMwu8vds4aGIMHZnNbdpSWCfZZtinytpcAvA== @@ -412,29 +412,6 @@ csstype "^3.1.2" prop-types "^15.8.1" -"@mui/styles@^5.14.5": - version "5.14.7" - resolved "https://registry.yarnpkg.com/@mui/styles/-/styles-5.14.7.tgz#e704f465b39e6dbfcd30090b191cf8140f7a9e42" - integrity sha512-5qA81gIRBUd3ur2FtGO10UmArpqaGWL+eUGFVSf68SjhahhHr86/JgqsXqUPyW/LPnyW92SZxhQ6El6Co8i7AQ== - dependencies: - "@babel/runtime" "^7.22.10" - "@emotion/hash" "^0.9.1" - "@mui/private-theming" "^5.14.7" - "@mui/types" "^7.2.4" - "@mui/utils" "^5.14.7" - clsx "^2.0.0" - csstype "^3.1.2" - hoist-non-react-statics "^3.3.2" - jss "^10.10.0" - jss-plugin-camel-case "^10.10.0" - jss-plugin-default-unit "^10.10.0" - jss-plugin-global "^10.10.0" - jss-plugin-nested "^10.10.0" - jss-plugin-props-sort "^10.10.0" - jss-plugin-rule-value-function "^10.10.0" - jss-plugin-vendor-prefixer "^10.10.0" - prop-types "^15.8.1" - "@mui/system@^5.14.7": version "5.14.7" resolved "https://registry.yarnpkg.com/@mui/system/-/system-5.14.7.tgz#b08e23f9151d38186ab12dd618906abd4d73d203" @@ -1652,14 +1629,6 @@ csrf@3.1.0: tsscmp "1.0.6" uid-safe "2.1.5" -css-vendor@^2.0.8: - version "2.0.8" - resolved "https://registry.yarnpkg.com/css-vendor/-/css-vendor-2.0.8.tgz#e47f91d3bd3117d49180a3c935e62e3d9f7f449d" - integrity sha512-x9Aq0XTInxrkuFeHKbYC7zWY8ai7qJ04Kxd9MnvbC1uO5DagxoHQjm4JvG+vCdXOoFtCjbL2XSZfxmoYa9uQVQ== - dependencies: - "@babel/runtime" "^7.8.3" - is-in-browser "^1.0.2" - cssesc@^3.0.0: version "3.0.0" resolved "https://registry.yarnpkg.com/cssesc/-/cssesc-3.0.0.tgz#37741919903b868565e1c09ea747445cd18983ee" @@ -2825,11 +2794,6 @@ human-signals@^4.3.0: resolved "https://registry.yarnpkg.com/human-signals/-/human-signals-4.3.1.tgz#ab7f811e851fca97ffbd2c1fe9a958964de321b2" integrity sha512-nZXjEF2nbo7lIw3mgYjItAfgQXog3OjJogSbKa2CQIIvSGWcKgeJnQlNXip6NglNzYH45nSRiEVimMvYL8DDqQ== -hyphenate-style-name@^1.0.3: - version "1.0.4" - resolved "https://registry.yarnpkg.com/hyphenate-style-name/-/hyphenate-style-name-1.0.4.tgz#691879af8e220aea5750e8827db4ef62a54e361d" - integrity sha512-ygGZLjmXfPHj+ZWh6LwbC37l43MhfztxetbFCoYTM2VjkIUpeHgSNn7QIyVFj7YQ1Wl9Cbw5sholVJPzWvC2MQ== - 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