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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,178 @@ | ||
| "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 { TfMotifTrack } from "./tfmotiftrack" | ||
| import { DenseBigBed, EmptyTrack, FullBigWig } from "umms-gb" | ||
|
|
||
| type TfSequenceFeaturesProps = { | ||
| coordinates: { | ||
| start: number | ||
| end: number | ||
| chromosome?: string | ||
| } | ||
| assembly: string | ||
| } | ||
| const GENE_QUERY = gql` | ||
| query s($chromosome: String, $start: Int, $end: Int, $assembly: String!) { | ||
| gene(chromosome: $chromosome, start: $start, end: $end, assembly: $assembly) { | ||
| name | ||
| strand | ||
| transcripts { | ||
| name | ||
| strand | ||
| exons { | ||
| coordinates { | ||
| chromosome | ||
| start | ||
| end | ||
| } | ||
| } | ||
| coordinates { | ||
| chromosome | ||
| start | ||
| end | ||
| } | ||
| } | ||
| } | ||
| } | ||
| ` | ||
| export type Transcript = { | ||
| id: string | ||
| name: string | ||
| strand: string | ||
| coordinates: GenomicRange | ||
| } | ||
| export type SNPQueryResponse = { | ||
| gene: { | ||
| name: string | ||
| strand: string | ||
| transcripts: Transcript[] | ||
| }[] | ||
| } | ||
| export function expandCoordinates(coordinates, l = 0) { | ||
| return { | ||
| chromosome: coordinates.chromosome, | ||
| start: coordinates.start - l < 0 ? 0 : coordinates.start - l, | ||
| end: coordinates.end + l, | ||
| } | ||
| } | ||
| const DATA_QUERY = ` | ||
| query q($requests: [BigRequest!]!) { | ||
| bigRequests(requests: $requests) { | ||
| data | ||
| } | ||
| } | ||
| ` | ||
|
|
||
| export const TfSequenceFeatures: React.FC<TfSequenceFeaturesProps> = (props) => { | ||
| const [data, setData] = useState([]) | ||
| const [loading, setLoading] = useState(true) | ||
| const svgRef = useRef<SVGSVGElement>(null) | ||
| const expandedCoordinates = useMemo(() => expandCoordinates(props.coordinates), [props.coordinates]) | ||
| const [coordinates, setCoordinates] = useState<GenomicRange>(expandedCoordinates) | ||
| useEffect(() => { | ||
| fetch("https://ga.staging.wenglab.org/graphql", { | ||
| method: "POST", | ||
| headers: { | ||
| "Content-Type": "application/json", | ||
| Accept: "application/json", | ||
| }, | ||
| body: JSON.stringify({ | ||
| query: DATA_QUERY, | ||
| variables: { | ||
| requests: [ | ||
| { | ||
| url: "gs://gcp.wenglab.org/SCREEN/all-sites.sorted.formatted.bigBed", | ||
| chr1: coordinates.chromosome, | ||
| start: coordinates.start, | ||
| chr2: coordinates.chromosome, | ||
| end: coordinates.end | ||
| }, | ||
| ], | ||
| }, | ||
| }), | ||
| }) | ||
| .then((x) => x.json()) | ||
| .then((x) => { | ||
| setData(x.data.bigRequests[0].data.filter((x) => x.name.split("$")[3] === "True")) | ||
| setLoading(false) | ||
| }) | ||
| }, [coordinates]) | ||
| console.log(data,'data') | ||
| const snpResponse = useQuery<SNPQueryResponse>(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: "#aaaaaa", | ||
| })), | ||
| })), | ||
| [snpResponse] | ||
| ) | ||
| 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] | ||
| ) | ||
| return ( | ||
| <> | ||
| <Grid2 container spacing={3} sx={{ mt: "1rem", mb: "1rem" }}> | ||
| <Grid2 xs={12} lg={12}> | ||
| <br /> | ||
| <CytobandView innerWidth={1000} height={15} chromosome={coordinates.chromosome!} assembly={props.assembly!=="mm10"? "hg38": "mm10"} position={coordinates} /> | ||
| <br /> | ||
| <div style={{ textAlign: "center" }}> | ||
| <Controls onDomainChanged={onDomainChanged} domain={coordinates || props.coordinates} /> | ||
| </div> | ||
| <br /> | ||
| <br /> | ||
| <GenomeBrowser | ||
| svgRef={svgRef} | ||
| domain={coordinates} | ||
| innerWidth={1400} | ||
| width="100%" | ||
| noMargin | ||
| onDomainChanged={(x) => { | ||
| if (Math.ceil(x.end) - Math.floor(x.start) > 10) { | ||
| setCoordinates({ | ||
| chromosome: coordinates.chromosome, | ||
| start: Math.floor(x.start), | ||
| end: Math.ceil(x.end), | ||
| }) | ||
| } | ||
| }} | ||
| > | ||
| <RulerTrack domain={coordinates} height={30} width={1400} /> | ||
| <EGeneTracks | ||
| genes={groupedTranscripts || []} | ||
| expandedCoordinates={coordinates} | ||
| squish={true} | ||
| /> | ||
| {!loading && data && props.assembly!=="mm10" && <TfMotifTrack width={1400} data={data} svgRef={svgRef} coordinates={coordinates}/>} | ||
|
|
||
| </GenomeBrowser> | ||
| </Grid2> | ||
| </Grid2> | ||
| </> | ||
| ) | ||
| } |
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