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 be152630..f5157a76 100644 --- a/screen2.0/package.json +++ b/screen2.0/package.json @@ -41,9 +41,9 @@ "@emotion/styled": "^11.11.0", "@mui/icons-material": "^5.14.3", "@mui/lab": "^5.0.0-alpha.137", - "@mui/material": "^5.14.2", - "@types/node": "^20.5.0", - "@types/react": "^18.2.20", + "@mui/material": "^5.14.2", + "@types/node": "^20.4.9", + "@types/react": "^18.2.19", "@types/react-dom": "18.2.7", "@weng-lab/psychscreen-ui-components": "^0.8.0-a.2", "@weng-lab/ts-ztable": "^4.0.1", @@ -56,13 +56,16 @@ "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", "react-dropzone": "^14.2.3", "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/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/page.tsx b/screen2.0/src/app/page.tsx index bc4209e7..3bae89b9 100644 --- a/screen2.0/src/app/page.tsx +++ b/screen2.0/src/app/page.tsx @@ -2,7 +2,8 @@ "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/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/ccresearch.tsx b/screen2.0/src/app/search/ccresearch.tsx index 14a37190..0d99ff20 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" @@ -7,14 +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" import { MainResultTableRows } from "./types" export const StyledTab = styled(Tab)(() => ({ textTransform: "none", })) export const CcreSearch = (props: { mainQueryParams, ccrerows: MainResultTableRows, 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) } @@ -45,13 +46,28 @@ export const CcreSearch = (props: { mainQueryParams, ccrerows: MainResultTableRo - + setTabIndex(val)}> + + + + + {tabIndex === 1 && ( + + )} + {tabIndex === 0 && ( + + )} )} 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..05528a6d --- /dev/null +++ b/screen2.0/src/app/search/gbview/allmotifs.ts @@ -0,0 +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, 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, 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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], + ], +} 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..88e881e6 --- /dev/null +++ b/screen2.0/src/app/search/gbview/biosampletracks.tsx @@ -0,0 +1,133 @@ +import { useQuery } from "@apollo/client" +import { associateBy } from "queryz" + +import React, { RefObject, useEffect, useMemo, useState } from "react" +import { EmptyTrack } from "umms-gb" +import { client } from "../ccredetails/client" +import { TitledTrack } from "./defaulttracks" +import { BIOSAMPLE_QUERY, BIG_QUERY } from "./queries" +import { GenomicRange, BigQueryResponse } from "./types" + + +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 const COLOR_MAP: Map = new Map([ + ["DNase", "#06da93"], + ["H3K4me3", "#ff0000"], + ["H3K27ac", "#ffcd00"], + ["CTCF", "#00b0d0"], +]) + +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 as any) || [], + (x: any) => x.name, + (x: any) => ({ 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 new file mode 100644 index 00000000..2450c173 --- /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..c018eb4f --- /dev/null +++ b/screen2.0/src/app/search/gbview/controls.tsx @@ -0,0 +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 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..c2b633e6 --- /dev/null +++ b/screen2.0/src/app/search/gbview/cytobandview.tsx @@ -0,0 +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 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..972d147f --- /dev/null +++ b/screen2.0/src/app/search/gbview/defaulttracks.tsx @@ -0,0 +1,190 @@ +import { useQuery } from "@apollo/client" +import { associateBy } from "queryz" +import { BigWigData, BigBedData } from "bigwig-reader" +import React, { RefObject, useEffect, useMemo, useState } from "react" +import { DenseBigBed, EmptyTrack, FullBigWig } from "umms-gb" +import { client } from "../ccredetails/client" +import CCRETooltip from "./ccretooltip" +import { BIG_QUERY } from "./queries" +import { GenomicRange, BigQueryResponse, BigResponseData } from "./types" + + +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 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: { name: string}) => x.name, + (x: any) => ({ 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 new file mode 100644 index 00000000..7e12d12c --- /dev/null +++ b/screen2.0/src/app/search/gbview/egenetracks.tsx @@ -0,0 +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 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..c77ea9a2 --- /dev/null +++ b/screen2.0/src/app/search/gbview/genomebrowserview.tsx @@ -0,0 +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/${result.ctcf_signal}.bigWig`, + "CTCF", + ]) + setTracks(tracks) + } + }, [bdata, props.biosample,props.assembly]) + return ( + <> + + +
+ +
+
+ +
+
+
+ { + if (Math.ceil(x.end) - Math.floor(x.start) > 10) { + setCoordinates({ + chromosome: coordinates.chromosome, + start: Math.floor(x.start), + end: Math.ceil(x.end), + }) + } + }} + > + {highlight && ( + + )} + + = 500000 ? true : false} + /> + + x && setHighlight(x)} + oncCREMousedOut={() => setHighlight(null)} + /> + {props.biosample && props.assembly != "mm10" && cTracks && ( + x && setHighlight(x)} + oncCREMousedOut={() => setHighlight(null)} + /> + )} + +
+
+ + ) +} diff --git a/screen2.0/src/app/search/gbview/queries.ts b/screen2.0/src/app/search/gbview/queries.ts new file mode 100644 index 00000000..46216dab --- /dev/null +++ b/screen2.0/src/app/search/gbview/queries.ts @@ -0,0 +1,30 @@ +import { gql } from "@apollo/client" +export const BIG_QUERY = gql` + query BigRequests($bigRequests: [BigRequest!]!) { + bigRequests(requests: $bigRequests) { + data + error { + errortype + message + } + } + } +` + +export const BIOSAMPLE_QUERY = gql` + query q($assembly: String!) { + ccREBiosampleQuery(assembly: $assembly) { + biosamples { + name + dnase: experimentAccession(assay: "DNase") + h3k4me3: experimentAccession(assay: "H3K4me3") + h3k27ac: experimentAccession(assay: "H3K27ac") + ctcf: experimentAccession(assay: "CTCF") + dnase_signal: fileAccession(assay: "DNase") + h3k4me3_signal: fileAccession(assay: "H3K4me3") + h3k27ac_signal: fileAccession(assay: "H3K27ac") + ctcf_signal: fileAccession(assay: "CTCF") + } + } + } +` diff --git a/screen2.0/src/app/search/gbview/shiftbutton.tsx b/screen2.0/src/app/search/gbview/shiftbutton.tsx new file mode 100644 index 00000000..45e16ea3 --- /dev/null +++ b/screen2.0/src/app/search/gbview/shiftbutton.tsx @@ -0,0 +1,32 @@ +import React from "react" +import { Button } from "@mui/material" +export interface Domain { + chromosome?: string + start: number + end: number +} + +export type ShiftButtonProps = { + text: string + shift: number + domain: Domain + onClick: (domain: Domain) => void +} + +const ShiftButton = ({ text, shift, domain, onClick }) => { + return ( + <> + + + ) +} +export default ShiftButton diff --git a/screen2.0/src/app/search/gbview/tfmotiftrack.tsx b/screen2.0/src/app/search/gbview/tfmotiftrack.tsx new file mode 100644 index 00000000..f086dacc --- /dev/null +++ b/screen2.0/src/app/search/gbview/tfmotiftrack.tsx @@ -0,0 +1,75 @@ +import React, { useState, useRef } from "react" +import { EmptyTrack, SquishBigBed } from "umms-gb" +import { DNALogo, Y } from "logots-react" +import { MOTIFS } from "./allmotifs" +import { Typography } from "@mui/material" +export type GenomicRange = { + chromosome?: string + start: number + end: number +} + +const MotifTooltip = (props) => { + const rc = (x) => [...x].map((xx) => [...xx].reverse()).reverse() + return ( +
+ {props.rectname.split("$")[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) => { + + return + }} + onClick={(x: any) => { + + 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/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/gbview/zoombutton.tsx b/screen2.0/src/app/search/gbview/zoombutton.tsx new file mode 100644 index 00000000..a7e09131 --- /dev/null +++ b/screen2.0/src/app/search/gbview/zoombutton.tsx @@ -0,0 +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 diff --git a/screen2.0/src/app/search/page.tsx b/screen2.0/src/app/search/page.tsx index 28832146..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 @@ -15,6 +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 36a10f71..2fa5844c 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/Footer.tsx b/screen2.0/src/common/components/Footer.tsx index 2109f990..727f219b 100644 --- a/screen2.0/src/common/components/Footer.tsx +++ b/screen2.0/src/common/components/Footer.tsx @@ -1,5 +1,5 @@ "use client" -import { Typography, Container, Box } from "@mui/material" +import { Typography, Box } from "@mui/material" import MuiLink from "@mui/material/Link" @@ -25,4 +25,4 @@ export default function Footer() { ) -} +} \ No newline at end of file diff --git a/screen2.0/src/common/components/MainResultsTable.tsx b/screen2.0/src/common/components/MainResultsTable.tsx index 3e37ad5e..cf94e1b4 100644 --- a/screen2.0/src/common/components/MainResultsTable.tsx +++ b/screen2.0/src/common/components/MainResultsTable.tsx @@ -1,7 +1,7 @@ "use client" import { DataTable, DataTableProps, DataTableColumn } from "@weng-lab/psychscreen-ui-components" -import React, { useCallback, useEffect, useState } from "react" -import { Box, Typography, Menu, Checkbox, Stack, MenuItem, Container, FormControlLabel, FormGroup } from "@mui/material" +import React, { useCallback, useState } from "react" +import { Box, Typography, Menu, Checkbox, Stack, MenuItem, FormControlLabel, FormGroup } from "@mui/material" import { MainResultTableRow } from "../../app/search/types" import ArrowRightIcon from '@mui/icons-material/ArrowRight'; import { usePathname, useRouter, useSearchParams } from "next/navigation" @@ -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.tsx b/screen2.0/src/common/components/MainSearch.tsx deleted file mode 100644 index fccf80a4..00000000 --- a/screen2.0/src/common/components/MainSearch.tsx +++ /dev/null @@ -1,78 +0,0 @@ -"use client" -import * as React from "react" - -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" - -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 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 ( - - { - if (event.code === "Enter") { - handleSubmit() - } - }} - InputProps={{ - endAdornment: ( - - handleSubmit()}> - - - - ), - }} - sx={{ mr: "1em" }} - /> - setChecked(checked)} - /> - - ) -} - -export default MainSearch diff --git a/screen2.0/src/common/components/ResponsiveAppBar.tsx b/screen2.0/src/common/components/ResponsiveAppBar.tsx index df6d8838..34e2a55e 100644 --- a/screen2.0/src/common/components/ResponsiveAppBar.tsx +++ b/screen2.0/src/common/components/ResponsiveAppBar.tsx @@ -1,47 +1,20 @@ "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 HeaderSearch from "./HeaderSearch" + /* Links for the AppBar. If adding another page with subpages, you need to add another useState() hook for positioning, and add extra if case in open/close handlers @@ -273,9 +246,11 @@ function ResponsiveAppBar() { ))} {/* TODO onSubmit for search box */} + + {/* Settings */} {/* = (props) => { + 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) => { + setOptions([]) + 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 + }, + }), + headers: { "Content-Type": "application/json" }, + }) + const ccreSuggestion = (await response.json()).data?.cCREQuery + if (ccreSuggestion && ccreSuggestion.length > 0) { + 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, + end: g.coordinates.end, + ccreaccession: g.accession, + } + }) + setOptions(r) + setCcreAccessions(ccres) + } else if (ccreSuggestion && ccreSuggestion.length === 0) { + setOptions([]) + setCcreAccessions([]) + } + } + + const debounceFn = useCallback(debounce(onSearchChange, 500), []) + + return ( + + + { + if (event.key === "Enter") { + event.defaultPrevented = true + + if (value) { + 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=${value}`) + } + } + }} + value={value} + onChange={(_, newValue: string | null) => { + setValue(newValue) + }} + inputValue={inputValue} + onInputChange={(event, newInputValue) => { + if (newInputValue != "") { + debounceFn(newInputValue) + } + + setInputValue(newInputValue) + }} + noOptionsText={props.assembly==="mm10"? "e.g EM10E0000207": "e.g. EH38E0001314"} + renderInput={(params) => ( + + )} + renderOption={(props, option) => { + return ( +
  • + + + + {option} + + {ccreAccessions && ccreAccessions.find((g: {ccreaccession: string }) => g.ccreaccession === option) && ( + + {`${(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 new file mode 100644 index 00000000..c4788ecf --- /dev/null +++ b/screen2.0/src/common/components/mainsearch/CelltypeAutocomplete.tsx @@ -0,0 +1,129 @@ +import React, { useState, 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 { useRouter } from "next/navigation" +import Config from "../../../config.json" + +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 router = useRouter() + + useEffect(() => { + fetch(props.assembly.toLowerCase()==="grch38" ? Config.API.HumanGlobals : Config.API.MouseGlobals) + .then((response) => { + return response.json() + }) + .then((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) + }) + .catch((error: Error) => { + console.log(error) + }) + + }, [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] + 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=${biosample}` + ) + } + } + }} + value={value} + onChange={(_, newValue: string | null) => { + setValue(newValue) + }} + inputValue={inputValue} + onInputChange={(_, newInputValue) => { + setValue(newInputValue) + setInputValue(newInputValue) + }} + noOptionsText={props.assembly==="mm10" ? "strain B6NCrl cortical plate tissue male adult (8 weeks)" :"e.g. LNCAP"} + renderInput={(params) => ( + + )} + renderOption={(props, option) => { + return ( +
  • + + + + {option} + + {cellTypes && cellTypes.find((g) => g.biosample_summary === option) && ( + + {`${cellTypes.find((g) => g.biosample_summary === option)?.tissue}`} + + )} + + +
  • + ) + }} + /> +
    +
    + ) +} diff --git a/screen2.0/src/common/components/mainsearch/GeneAutocomplete.tsx b/screen2.0/src/common/components/mainsearch/GeneAutocomplete.tsx new file mode 100644 index 00000000..bffff67d --- /dev/null +++ b/screen2.0/src/common/components/mainsearch/GeneAutocomplete.tsx @@ -0,0 +1,167 @@ +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" +import Grid from "@mui/material/Grid" +import Typography from "@mui/material/Typography" +import { debounce } from "@mui/material/utils" +import { useRouter } from "next/navigation" +import { GENE_AUTOCOMPLETE_QUERY } from "./queries" +import Config from "../../../config.json" +type QueryResponse = [number, string[], any, [string, string, string, string, string, string][], string[]] + +export const GeneAutoComplete: React.FC<{assembly: string, textColor: string }> = (props) => { + 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] = useState<{ name: string; desc: string }[]>() + + 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(Config.API.GraphqlAPI, { + method: "POST", + body: JSON.stringify({ + query: GENE_AUTOCOMPLETE_QUERY, + variables: { + assembly: props.assembly.toLowerCase(), + 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 = useCallback(debounce(onSearchChange, 500), []) + const gridsize = 5.5 + return ( + + + { + if (event.key === "Enter") { + event.defaultPrevented = true + + + 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={(_, newValue: string | null) => { + setValue(newValue) + }} + inputValue={inputValue} + onInputChange={(_, 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/mainsearch/SnpAutocomplete.tsx b/screen2.0/src/common/components/mainsearch/SnpAutocomplete.tsx new file mode 100644 index 00000000..37ca48e1 --- /dev/null +++ b/screen2.0/src/common/components/mainsearch/SnpAutocomplete.tsx @@ -0,0 +1,141 @@ +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 { SNP_AUTOCOMPLETE_QUERY } from "./queries" +import Config from "../../../config.json" + +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([]) + const [snpids, setSnpIds] = React.useState([]) + const router = useRouter() + + const onSearchChange = async (value: string) => { + setOptions([]) + const response = await fetch(Config.API.GraphqlAPI, { + method: "POST", + body: JSON.stringify({ + query: SNP_AUTOCOMPLETE_QUERY, + variables: { + assembly: props.assembly.toLowerCase(), + snpid: value, + }, + }), + headers: { "Content-Type": "application/json" }, + }) + const snpSuggestion = (await response.json()).data?.snpAutocompleteQuery + if (snpSuggestion && snpSuggestion.length > 0) { + 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, + end: g.coordinates.end, + id: g.id, + } + }) + setOptions(r) + setSnpIds(snp) + } else if (snpSuggestion && snpSuggestion.length === 0) { + setOptions([]) + setSnpIds([]) + } + + } + + 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=${value}` + ) + } + } + }} + value={value} + onChange={(_, newValue: string | null) => { + setValue(newValue) + }} + inputValue={inputValue} + onInputChange={(_, newInputValue) => { + if (newInputValue != "") { + debounceFn(newInputValue) + } + + setInputValue(newInputValue) + }} + noOptionsText="e.g. rs11669173" + renderInput={(params) => ( + + )} + renderOption={(props, option) => { + return ( +
  • + + + + {option} + + {snpids && snpids.find((g) => g.id === option) && ( + + {`${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/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 b6f44525..21fcc30f 100644 --- a/screen2.0/yarn.lock +++ b/screen2.0/yarn.lock @@ -1,8137 +1,5465 @@ -# 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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