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added CRISPR fcc data #607

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Merged
jpfisher72 merged 1 commit into from
Jul 9, 2025
Merged

added CRISPR fcc data #607

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106 changes: 96 additions & 10 deletions screen2.0/src/app/search/_ccredetails/functionaldata.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -2,19 +2,25 @@
import React from "react"
import { client } from "./client"
import { useQuery } from "@apollo/client"
import { FUNCTIONAL_DATA_QUERY, CCRE_RDHS_QUERY, MPRA_FUNCTIONAL_DATA_QUERY, CAPRA_SOLO_FUNCTIONAL_DATA_QUERY, CAPRA_DOUBLE_FUNCTIONAL_DATA_QUERY } from "./queries"
import { FUNCTIONAL_DATA_QUERY, CCRE_RDHS_QUERY, MPRA_FUNCTIONAL_DATA_QUERY, CAPRA_SOLO_FUNCTIONAL_DATA_QUERY, CAPRA_DOUBLE_FUNCTIONAL_DATA_QUERY, CRISPR_FUNCTIONAL_DATA_QUERY } from "./queries"
import Grid from "@mui/material/Grid2"
import { DataTable } from "@weng-lab/psychscreen-ui-components"
import { LoadingMessage, ErrorMessage, CreateLink } from "../../../common/lib/utility"
import { Link } from "@mui/material"

type ExperimentInfo = {
type CAPRA_ExperimentInfo = {
lab: string;
cellType: string;
};

type CRISPR_ExperimentInfo = {
lab: string;
cellType: string;
design: string;
};

// Define the map where experiment is the key
const capra_experimentMap: Record<string, ExperimentInfo> = {
const capra_experimentMap: Record<string, CAPRA_ExperimentInfo> = {
"ENCSR064KUD": { lab: "Kevin White, UChicago", cellType: "HCT116" },
"ENCSR135NXN": { lab: "Kevin White, UChicago", cellType: "HepG2" },
"ENCSR547SBZ": { lab: "Kevin White, UChicago", cellType: "MCF-7" },
Expand All @@ -24,6 +30,20 @@ const capra_experimentMap: Record<string, ExperimentInfo> = {
"ENCSR983SZZ": { lab: "Kevin White, UChicago", cellType: "SH-SY5Y" }
};

const crispr_experimentMap: Record<string, CRISPR_ExperimentInfo> = {
"ENCSR179FSH": { design: "proliferation CRISPRi screen (dCas9-KRAB)", lab: "Tim Reddy, Duke", cellType: "OCI-AML2" },
"ENCSR274OEB": { design: "proliferation CRISPRi screen (dCas9-KRAB)", lab: "Tim Reddy, Duke", cellType: "K562" },
"ENCSR295VER": { design: "roliferation CRISPRi screen (dCas9-KRAB-WSR7EEE)", lab: "Will Greenleaf, Stanford", cellType: "K562" },
"ENCSR369UFO": { design: "proliferation CRISPRi screen (dCas9-RYBP)", lab: "Will Greenleaf, Stanford", cellType: "K562" },
"ENCSR372CKT": { design: "proliferation CRISPRi screen (dCas9-ZNF705-KRAB)", lab: "Will Greenleaf, Stanford", cellType: "K562" },
"ENCSR381RDB": { design: "proliferation CRISPRi screen (dCas9-RYBP)", lab: "Will Greenleaf, Stanford", cellType: "K562" },
"ENCSR386FFV": { design: "proliferation CRISPRi screen (dCas9-KRAB-WSR7EEE)", lab: "Will Greenleaf, Stanford", cellType: "K562" },
"ENCSR427OCU": { design: "proliferation CRISPRi screen (dCas9-KRAB-MGA1-MGA2)", lab: "Will Greenleaf, Stanford", cellType: "K562" },
"ENCSR446RYW": { design: "proliferation CRISPRi screen (dCas9-KRAB)", lab: "Will Greenleaf, Stanford", cellType: "K562" },
"ENCSR690DTG": { design: "proliferation CRISPRi screen (dCas9-KRAB)", lab: "Tim Reddy, Duke", cellType: "K562" },
"ENCSR997ZOY": { design: "proliferation CRISPRi screen (dCas)", lab: "Will Greenleaf, Stanford", cellType: "K562" }
};

export const FunctionData = ({ coordinates , assembly, accession }) => {
const { loading, error, data } = useQuery(FUNCTIONAL_DATA_QUERY, {
variables: {
Expand All @@ -44,6 +64,15 @@ export const FunctionData = ({ coordinates , assembly, accession }) => {
nextFetchPolicy: "cache-first",
client,
})
const { loading: crispr_loading, error: crispr_error, data: crispr_data } = useQuery(CRISPR_FUNCTIONAL_DATA_QUERY, {
variables: {
accession: [accession],
},
skip: assembly === "mm10",
fetchPolicy: "cache-and-network",
nextFetchPolicy: "cache-first",
client,
})
const { loading: capra_loading, error: capra_error, data: capra_data } = useQuery(CAPRA_SOLO_FUNCTIONAL_DATA_QUERY, {
variables: {
accession: [accession],
Expand All @@ -53,6 +82,7 @@ export const FunctionData = ({ coordinates , assembly, accession }) => {
nextFetchPolicy: "cache-first",
client,
})

const { loading: capra_double_loading, error: capra_double_error, data: capra_double_data } = useQuery(CAPRA_DOUBLE_FUNCTIONAL_DATA_QUERY, {
variables: {
accession: [accession],
Expand All @@ -63,20 +93,20 @@ export const FunctionData = ({ coordinates , assembly, accession }) => {
client,
})


//CCRE_RDHS_QUERY
const { loading: capra_double_rdhs_loading, error: capra_double_rdhs_error, data: capra_double_rdhs_data } = useQuery(CCRE_RDHS_QUERY, {
variables: {
assembly: "GRCh38",
rDHS: [capra_double_data && capra_double_data.capraFccDoubleQuery.length>0 &&capra_double_data.capraFccDoubleQuery[0].rdhs_p1,capra_double_data && capra_double_data.capraFccDoubleQuery.length>0 && capra_double_data.capraFccDoubleQuery[0].rdhs_p2],
},
//capra_double_data.capraFccDoubleQuery[0].rdhs_p1,capra_double_data.capraFccDoubleQuery[0].rdhs_p2
skip: capra_double_data===undefined || !capra_double_data ,
rDHS: [capra_double_data && capra_double_data.capraFccDoubleQuery.length>0 && capra_double_data.capraFccDoubleQuery[0].rdhs_p1,capra_double_data && capra_double_data.capraFccDoubleQuery.length>0 && capra_double_data.capraFccDoubleQuery[0].rdhs_p2],
},
skip: capra_double_data===undefined || !capra_double_data || (capra_double_data && capra_double_data.capraFccDoubleQuery.length===0) ,
fetchPolicy: "cache-and-network",
nextFetchPolicy: "cache-first",
client,
})

return loading || mpra_loading || capra_loading || capra_double_loading || capra_double_rdhs_loading? (
return loading || mpra_loading || crispr_loading || capra_loading || capra_double_loading || capra_double_rdhs_loading? (
<LoadingMessage />
) : error ? (
<ErrorMessage error={error} />
Expand Down Expand Up @@ -262,10 +292,10 @@ export const FunctionData = ({ coordinates , assembly, accession }) => {
itemsPerPage={5}
/>
</Grid>}</>}
{ capra_double_error ? (
{ capra_double_error ? (
<ErrorMessage error={capra_double_error} />
) : <>
{assembly!=="mm10" &&<Grid
{assembly!=="mm10" && <Grid
size={{
xs: 12,
md: 12,
Expand Down Expand Up @@ -335,6 +365,62 @@ export const FunctionData = ({ coordinates , assembly, accession }) => {
itemsPerPage={5}
/>
</Grid>}</>}

{ crispr_error ? (
<ErrorMessage error={crispr_error} />
) : <>
{assembly!=="mm10" && <Grid
size={{
xs: 12,
md: 12,
lg: 12
}}>
<DataTable
tableTitle={`CRISPR perturbation data`}
columns={[
{
header: "Experiment",
value: (row) => row.experiment,
render: (row) => <CreateLink
linkPrefix="https://www.encodeproject.org/experiments/"
linkArg={row.experiment}
label={row.experiment}
showExternalIcon
underline="always"
/>
},
{
header: "Design",
value: (row) => crispr_experimentMap[row.experiment].design,
},
{
header: "Celltype",
value: (row) => crispr_experimentMap[row.experiment].cellType,
},
{
header: "Lab",
value: (row) => crispr_experimentMap[row.experiment].lab,
},
{
header: "Log2(Fold Change)",
HeaderRender: () => <>Log<sub>2</sub>(Fold Change)</>,
value: (row) => row.log2fc.toFixed(2),
},
{
header: "P",
value: (row) => !row.pvalue ? "n/a" : row.pvalue.toFixed(2),
HeaderRender: () => <i>P</i>,
},
{
header: "FDR",
value: (row) => !row.fdr ? "n/a" : row.fdr.toFixed(2),
}
]}
rows={crispr_data.crisprFccQuery || []}
sortColumn={4}
itemsPerPage={5}
/>
</Grid>}</>}
</Grid>
);
}
13 changes: 13 additions & 0 deletions screen2.0/src/app/search/_ccredetails/queries.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -87,6 +87,19 @@ query MPRA_FCC($coordinates: [GenomicRangeInput!]) {
}
}
`)

export const CRISPR_FUNCTIONAL_DATA_QUERY = gql(`
query crisprFccQuery($accession: [String]!) {
crisprFccQuery(accession: $accession) {
rdhs
log2fc
fdr
pvalue
experiment
}
}
`)

export const CAPRA_SOLO_FUNCTIONAL_DATA_QUERY = gql(`
query capraFccSoloQuery($accession: [String]!) {
capraFccSoloQuery(accession: $accession) {
Expand Down
6 changes: 6 additions & 0 deletions screen2.0/src/graphql/__generated__/gql.ts
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