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multiple updates, esp. to cohorts & subsets pages
... also fix for variant identifier referencing
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,111 @@ | ||
| import { | ||
| SITE_DEFAULTS, | ||
| useServiceItemDelivery, | ||
| sampleSearchPageFiltersLink, | ||
| NoResultsHelp | ||
| } from "../hooks/api" | ||
| import { Loader } from "./Loader" | ||
| import { SubsetHistogram } from "./SVGloaders" | ||
| // import { ShowJSON } from "./RawData" | ||
| import { ExternalLink, InternalLink } from "./helpersShared/linkHelpers" | ||
|
|
||
| const service = "collations" | ||
|
|
||
| export function SubsetLoader({ id, datasetIds }) { | ||
| const { data, error, isLoading } = useServiceItemDelivery( | ||
| id, | ||
| service, | ||
| datasetIds | ||
| ) | ||
| return ( | ||
| <Loader isLoading={isLoading} hasError={error} background> | ||
| {data && ( | ||
| <SubsetResponse response={data} id={id} datasetIds={datasetIds} /> | ||
| )} | ||
| </Loader> | ||
| ) | ||
| } | ||
|
|
||
| function SubsetResponse({ response, datasetIds }) { | ||
| if (!response.response.results[0]) { | ||
| return NoResultsHelp("subsetdetails") | ||
| } | ||
| return <Subset subset={response.response.results[0]} datasetIds={datasetIds} /> | ||
| } | ||
|
|
||
| function Subset({ subset, datasetIds }) { | ||
|
|
||
| const filters = subset.id | ||
| const sampleFilterScope = "allTermsFilters" | ||
|
|
||
| return ( | ||
| <section className="content"> | ||
| <h2> | ||
| {subset.label} ({subset.id}) | ||
| </h2> | ||
|
|
||
| {subset.type && ( | ||
| <> | ||
| <h5>Subset Type</h5> | ||
| <ul> | ||
| <li> | ||
| {subset.type}{" "} | ||
| <ExternalLink | ||
| href={subset.reference} | ||
| label={subset.id} | ||
| /> | ||
| </li> | ||
| </ul> | ||
| </> | ||
| )} | ||
|
|
||
| <h5>Sample Counts</h5> | ||
| <ul> | ||
| <li>{subset.count} samples</li> | ||
| <li>{subset.codeMatches} direct <i>{subset.id}</i> code matches</li> | ||
| {subset.cnvAnalyses && ( | ||
| <li>{subset.cnvAnalyses} CNV analyses</li> | ||
| )} | ||
| {subset.frequencymapCnvAnalyses && ( | ||
| <li> | ||
| {subset.frequencymapCnvAnalyses} {" CNV analyses used in frequency calculations"} | ||
| </li> | ||
| )} | ||
| </ul> | ||
| <h5>CNV Histogram</h5> | ||
| <div className="mb-3"> | ||
| <SubsetHistogram | ||
| id={subset.id} | ||
| datasetIds={datasetIds} | ||
| loaderProps={{background: true, colored: true}} | ||
| /> | ||
| </div> | ||
|
|
||
| <h5> | ||
| <InternalLink | ||
| href={`${SITE_DEFAULTS.API_PATH}services/intervalFrequencies/${subset.id}/?output=pgxfreq`} | ||
| label="Download CNV frequencies" | ||
| /> | ||
| </h5> | ||
| <p> | ||
| Download CNV frequency data for genomic 1Mb bins. | ||
| </p> | ||
|
|
||
| <h5> | ||
| <InternalLink | ||
| href={ sampleSearchPageFiltersLink({datasetIds, sampleFilterScope, filters}) } | ||
| label={`Search for ${subset.id} Samples`} | ||
| rel="noreferrer" | ||
| target="_blank" | ||
| /> | ||
| </h5> | ||
| <p> | ||
| Select samples through the search form, e.g. by querying for specific | ||
| genomic variants or phenotypes. | ||
| </p> | ||
|
|
||
| {/*<ShowJSON data={subset} />*/} | ||
|
|
||
| </section> | ||
| ) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| import React from "react" | ||
| import { Layout } from "../../components/Layout" | ||
| import { SubsetLoader } from "../../components/SubsetLoader" | ||
| import Panel from "../../components/Panel" | ||
| import SubsetsHierarchyLoader from "../../components/SubsetsHierarchyLoader" | ||
|
|
||
| const datasetIds = "progenetix" | ||
| const subsetId = "pgx:cohort-TCGAcancers" | ||
|
|
||
| export default function arraymap_dataPage() { | ||
| return ( | ||
| <Layout title="TCGA Cancer Subsets" headline=""> | ||
| <Panel> | ||
| <SubsetLoader | ||
| id={subsetId} | ||
| datasetIds={datasetIds} | ||
| /> | ||
| </Panel> | ||
| <Panel> | ||
| <ThisSubset /> | ||
| </Panel> | ||
| <Panel heading="TCGA Cancer Studies"> | ||
| <SubsetsHierarchyLoader collationTypes="TCGAproject" datasetIds="progenetix" /> | ||
| </Panel> | ||
| </Layout> | ||
| ) | ||
| } | ||
|
|
||
| function ThisSubset() { | ||
| return ( | ||
| <> | ||
| <div style={{ display: "flex" }}> | ||
| This page represents the TCGA subset of the Progenetix | ||
| collection, based on 22142 samples (tumor and reeferences) from The | ||
| Cancer Genome Atlas project. The results are based upon data generated | ||
| by the TCGA Research Network. Disease-specific subsets of TCGA data (aka. projects) can be | ||
| accessed below. | ||
| <img | ||
| src={"/img/tcga.png"} | ||
| style={{ | ||
| float: "right", | ||
| width: "200px", | ||
| border: "0px", | ||
| margin: "-20px -20px 0px 0px" | ||
| }} | ||
| /> | ||
| </div> | ||
| </> | ||
| ) | ||
| } |
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