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adding overlap check (#1009)
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@pieterlukasse @m0nhawk
pieterlukasse authored and m0nhawk committed Aug 3, 2022
1 parent e7c56bd commit 736f922
Showing 1 changed file with 82 additions and 11 deletions.
93 changes: 82 additions & 11 deletions src/Analysis/GWASUIApp/CaseControlGWAS.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,7 @@ const CaseControlGWAS = (props) => {
const [controlCohortDefinitionId, setControlCohortDefinitionId] = useState(undefined);
const [selectedControlCohort, setSelectedControlCohort] = useState(undefined);
const [caseCohortName, setCaseCohortName] = useState(undefined);
const [controlCohortName, setControlCohortName] = useState(undefined);

const [covariateVars] = useState({
ConceptIds: [2000006886, 2000000280, 2000000895, 2000000914, 2000000900, 2000000846, 2000000872, 2000000873, 2000000874, 2000006885, 2000000708],
Expand All @@ -72,6 +73,9 @@ const CaseControlGWAS = (props) => {
const [numOfPC, setNumOfPC] = useState(3);
const [selectedCaseHare, setSelectedCaseHare] = useState("-select one-");
const [selectedControlHare, setSelectedControlHare] = useState("-select one-");
const [selectedCaseSize, setSelectedCaseSize] = useState(0);
const [selectedControlSize, setSelectedControlSize] = useState(0);

const [gwasJobName, setGwasJobName] = useState("");
const hareConceptId = 2000007027;

Expand Down Expand Up @@ -137,6 +141,7 @@ const CaseControlGWAS = (props) => {
onChange: (_, selectedRows) => {
setSelectedControlCohort(selectedRows[0]);
setControlCohortDefinitionId(selectedRows[0].cohort_definition_id);
setControlCohortName(selectedRows[0].cohort_name);
},
getCheckboxProps: (record) => ({
disabled: record.size === 0 || record.cohort_name === caseCohortName,
Expand Down Expand Up @@ -403,6 +408,16 @@ const CaseControlGWAS = (props) => {
return fetchConceptStatsByHare(controlCohortDefinitionId);
}

function setSelectedCaseSubsetDetails(concept_stats_for_value){
setSelectedCaseHare(concept_stats_for_value.concept_value);
setSelectedCaseSize(concept_stats_for_value.persons_in_cohort_with_value);
}

function setSelectedContolSubsetDetails(concept_stats_for_value){
setSelectedControlHare(concept_stats_for_value.concept_value);
setSelectedControlSize(concept_stats_for_value.persons_in_cohort_with_value);
}

const ConceptsStatsByHare = () => {
const results = useQueries([
{ queryKey: ['conceptsstats', selectedCovariates, caseCohortDefinitionId], queryFn: fetchCaseConceptStatsByHare, ...queryConfig },
Expand Down Expand Up @@ -440,7 +455,7 @@ const CaseControlGWAS = (props) => {
<Dropdown.Item
key={`${datum.concept_value}`}
value={`${datum.concept_value}`}
onClick={() => setSelectedCaseHare(datum.concept_value)
onClick={() => setSelectedCaseSubsetDetails(datum)
}
>
{<div>{datum.concept_value} {" (size:" + datum.persons_in_cohort_with_value + ")"}</div>}
Expand All @@ -461,7 +476,7 @@ const CaseControlGWAS = (props) => {
<Dropdown.Item
key={`${datum.concept_value}`}
value={`${datum.concept_value}`}
onClick={() => setSelectedControlHare(datum.concept_value)
onClick={() => setSelectedContolSubsetDetails(datum)
}
>
{<div>{datum.concept_value} {" (size:" + datum.persons_in_cohort_with_value + ")"}</div>}
Expand All @@ -476,6 +491,58 @@ const CaseControlGWAS = (props) => {
}
};

async function fetchOverlapInfo() {
var conceptIds = [...selectedCovariates].map((val) => val.concept_id);
const conceptIdsPayload = { ConceptIds: conceptIds };
const statsEndPoint = `${cohortMiddlewarePath}cohort-stats/check-overlap/by-source-id/${sourceId}/by-case-control-cohort-definition-ids/${caseCohortDefinitionId}/${controlCohortDefinitionId}/filter-by-concept-id-and-value/${hareConceptId}/${selectedCaseHare}`;
const reqBody = {
method: 'POST',
credentials: 'include',
headers,
body: JSON.stringify(conceptIdsPayload),
};
const getOverlapStats = await fetch(statsEndPoint, reqBody);
return getOverlapStats.json();
}

const QCShowOverlap = () => {
const { data, status } = useQuery(['checkoverlap', sourceId, caseCohortDefinitionId, controlCohortDefinitionId, hareConceptId, selectedCaseHare, selectedCovariates], fetchOverlapInfo, queryConfig);

if (status === 'loading') {
return <Spinner />;
}
if (status === 'error') {
return <React.Fragment>Error</React.Fragment>;
}

if (data.cohort_overlap.case_control_overlap_after_filter === 0) {
return (
<div className="GWASUI-flexCol">
Based on the selected covariates their respective data within the study population,<br/>
{selectedCaseSize} subjects were found in {caseCohortName} cohort and <br/>
{selectedControlSize} subjects were found in {controlCohortName} cohort.<br/>
<strong style={{color: '#006644'}}>No overlap found between both cohorts.</strong>
</div>
);
} else {
// display an error message if there is any overlap between case and control populations:
return (
<div className="GWASUI-flexCol">
Based on the selected covariates their respective data within the study population,<br/>
{selectedCaseSize} subjects were found in <b>{caseCohortName}</b> cohort and <br/>
{selectedControlSize} subjects were found in <b>{controlCohortName}</b> cohort.<br/>
<strong style={{color: '#bf2600'}}>Warning: overlap found between both cohorts!<br/>
({data.cohort_overlap.case_control_overlap_after_filter} subjects were found to be present in both cohorts).<br/>
Please review your selections.<br/>
If you choose to continue, be aware that these {data.cohort_overlap.case_control_overlap_after_filter} subjects will <i>not</i> be considered in the analysis.
</strong>
</div>
);

}

};

async function fetchGwasSubmit() {
const submitEndpoint = `${gwasWorkflowPath}submit`;
const requestBody = {
Expand Down Expand Up @@ -510,6 +577,7 @@ const CaseControlGWAS = (props) => {
setCaseCohortDefinitionId(undefined);
setControlCohortDefinitionId(undefined);
setCaseCohortName(undefined);
setControlCohortName(undefined);
setSelectedControlCohort(undefined);
setSelectedCaseCohort(undefined);
setSelectedCaseHare("-select one-");
Expand Down Expand Up @@ -644,16 +712,19 @@ const CaseControlGWAS = (props) => {
<div className="GWASUI-flexCol GWASUI-flexHeader2">Selected Control Cohort</div>
<div className="GWASUI-flexCol">{selectedControlCohort?.cohort_name}</div>
</div>
<div className="GWASUI-flexRow">
<div className="GWASUI-flexCol GWASUI-rowItem">Covariates</div>
<div className="GWASUI-flexRow GWASUI-rowItem">
<div className="GWASUI-flexCol">Covariates</div>
<div className="GWASUI-flexCol">{selectedCovariates.map((cov, key) => {
return (
<div>
<li className="GWASUI-listItem" key={key}>{cov.concept_name}</li>
</div>
)
})}</div>
</div>
<div className="GWASUI-flexRow GWASUI-rowItem">
<QCShowOverlap/>
</div>
<div className="GWASUI-flexRow">{selectedCovariates.map((cov, key) => {
return (
<div>
<li className="GWASUI-listItem" key={key}>{cov.concept_name}</li>
</div>
)
})}</div>
<div className="GWASUI-flexRow">
<input
type="text"
Expand Down

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