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Gene expression app & RAMPAGE tab (#76)
* initial upload, added fetch, buttons, title * added types for gene exp * added expression plot, fixed buttons, and added gene autocomplete * fixed gene autocomplete * added rampage tab and adjusted spacing * fixed scaling and adjusted dimensions * changed tab name * added sort, zero switch, and transcript select * formatted numbers * spacing, prettier * change rampage tab name * added dropdowns to graph, added drawer, and fixed scaling * added settings * replaced details tab with hamburger * updated error logger * hyperlinked genes in main table * added gene expression tab to details * upated types * added collapse all, removed outline, and fixed scaling * added toolbar, added url nav, fixed search, and added collapse all * added header and updated descriptions * adjusted buttons / spacing, fixed plot scaling, and added collapse all * prettier * fixed link pathname and error utility * added keys, cleaned types * fixed hamburger height and width, cleaned types * changed error util * changed default export for build * moved gene-expression tab * fixed default export * fixed error handler * rerun checks * changed header color * added theme * fixed collapse all, changed theme * added all track colors * updated theme * updated theme * updated theme * cleaned up code, moved utils * replaced autocomplete with select * cleaned up * updated collapse all
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screen2.0/src/app/applets/gene-expression/gene-autocomplete.tsx
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,177 @@ | ||
| "use client" | ||
| import React, { useState, useEffect, useCallback } from "react" | ||
| import { useRouter } from "next/navigation" | ||
|
|
||
| import { Autocomplete, TextField, Box, Button, debounce, Typography } from "@mui/material" | ||
|
|
||
| import Grid2 from "@mui/material/Unstable_Grid2/Grid2" | ||
| import { gene } from "./types" | ||
| import { QueryResponse } from "../../../../types/types" | ||
| import { Dispatch, SetStateAction } from "react" | ||
|
|
||
| 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 default function GeneAutoComplete(props: { | ||
| assembly: string | ||
| gene: string | ||
| pathname: string | ||
| setGene: Dispatch<SetStateAction<string>> | ||
| }) { | ||
| const router = useRouter() | ||
|
|
||
| const [options, setOptions] = useState<string[]>([]) | ||
| const [geneDesc, setgeneDesc] = useState<{ name: string; desc: string }[]>() | ||
| const [geneList, setGeneList] = useState<gene[]>([]) | ||
| const [geneID, setGeneID] = useState<string>(props.gene ? props.gene : "OR51AB1P") | ||
| const [assembly, setAssembly] = useState<string>(props.assembly) | ||
| // const [current_gene, setGene] = useState<string>(props.gene ? props.gene : "OR51AB1P") | ||
|
|
||
| // gene descriptions | ||
| 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]) | ||
|
|
||
| // gene list | ||
| 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: props.assembly, | ||
| name_prefix: value, | ||
| limit: 100, | ||
| }, | ||
| }), | ||
| 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) | ||
| setGeneList(g) | ||
| } else if (genesSuggestion && genesSuggestion.length === 0) { | ||
| setOptions([]) | ||
| setGeneList([]) | ||
| } | ||
| } | ||
|
|
||
| // delay fetch | ||
| const debounceFn = useCallback(debounce(onSearchChange, 500), []) | ||
|
|
||
| return ( | ||
| <Box> | ||
| <Autocomplete | ||
| disablePortal | ||
| freeSolo={true} | ||
| id="gene-ids" | ||
| noOptionsText="e.g. Gm25142" | ||
| options={options} | ||
| size="small" | ||
| sx={{ width: 200 }} | ||
| ListboxProps={{ | ||
| style: { | ||
| maxHeight: "120px", | ||
| }, | ||
| }} | ||
| onChange={(event: React.ChangeEvent<HTMLInputElement>, value: string) => { | ||
| if (value != "") debounceFn(value) | ||
| setGeneID(value) | ||
| }} | ||
| onInputChange={(event: React.ChangeEvent<HTMLInputElement>, value: string) => { | ||
| if (value != "") debounceFn(value) | ||
| setGeneID(value) | ||
| }} | ||
| onKeyDown={(e) => { | ||
| if (e.key == "Enter") { | ||
| for (let g of geneList) { | ||
| if (g.name === geneID && g.end - g.start > 0) { | ||
| props.setGene(g.name) | ||
| // replace url if ge applet | ||
| if (props.pathname.split("/").includes("gene-expression")) router.replace(props.pathname + "?gene=" + g.name) | ||
| break | ||
| } | ||
| } | ||
| } | ||
| }} | ||
| renderInput={(props) => <TextField {...props} label={geneID} />} | ||
| renderOption={(props, opt) => { | ||
| return ( | ||
| <li {...props} key={props.id}> | ||
| <Grid2 container alignItems="center"> | ||
| <Grid2 sx={{ width: "calc(100% - 44px)" }}> | ||
| <Box component="span" sx={{ fontWeight: "regular" }}> | ||
| {opt} | ||
| </Box> | ||
| {geneDesc && geneDesc.find((g) => g.name === opt) && ( | ||
| <Typography variant="body2" color="text.secondary"> | ||
| {geneDesc.find((g) => g.name === opt)?.desc} | ||
| </Typography> | ||
| )} | ||
| </Grid2> | ||
| </Grid2> | ||
| </li> | ||
| ) | ||
| }} | ||
| /> | ||
| <Button | ||
| variant="text" | ||
| onClick={() => { | ||
| for (let g of geneList) { | ||
| if (g.name === geneID && g.end - g.start > 0) { | ||
| props.setGene(g.name) | ||
| // replace url if ge applet | ||
| if (props.pathname.split("/").includes("gene-expression")) router.replace(props.pathname + "?gene=" + g.name) | ||
| break | ||
| } | ||
| } | ||
| }} | ||
| color="primary" | ||
| > | ||
| Search | ||
| </Button> | ||
| </Box> | ||
| ) | ||
| } |
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