Gene coverage filter in Patient View mutation and CNA tables #2717

pvannierop · 2019-09-19T07:36:54Z

Note: this branch builds on top of branch patientview_genepanel_table_integration and the PR is to this branch for the reason of reviewing the code. This PR is therefore in draft mode.

What? Why?

As defined in RFC45 information on gene panels will be integrated in the PatientView component. Central problem with gene panels in patient view is the ambiguous interpretation of missing mutations in the mutation and copynumber tables. In these tables mutations in samples are represented as numbered sample icons in respective rows of each table. Absense of mutations and CNA's in the tables is indicated by:

a '?' icon when the gene was not profiled for the respective sample
no icon when the gene was profile in the sample

There is a use case where the user is only interested in investigating only those mutations that were profiled in all samples of a patient (has no '?' icons). At the moment the user has to idenitfy these mutations by eye among the other mutation rows in the table.

Fix

We have implemented a filter that allows the user to toggle between display of mutation present in ANY SAMPLE (default behavior) or ALL SAMPLES.
Filtering is performed independently for the mutation and CNA tables. Selection of ALL SAMPLES will filter the rows of the corresponding table and show only mutations for genes that were profiled in all samples of the patient.
The filter option is accessed via a filter icon in the header of the the Genes column. Clicking this icon will open a tooltip menu where the used can select the filter option in a radio menu. The menu is closed when the user again clicks the filter icon.
After filtering there is no visual cue presented to the user because the user is assumed to have selected the filter option consciously and because the default option is the display of all mutation rows.

Note: mutation and CNA genomic tracks will be updated depending on the gene filter setting. This feature will be implemented in a followup PR.

Preview

end-to-end-test/shared/specUtils.js

src/pages/patientView/PatientViewPage.tsx

src/pages/patientView/clinicalInformation/PatientViewPageStore.ts

src/pages/patientView/mutation/column/TumorColumnFormatter.tsx

src/pages/patientView/mutation/style.scss

adamabeshouse

nice!

pvannierop · 2019-10-08T11:54:39Z

As discussed in PR #2746 I added the conditional rendering of the filter menu icon.

In the mutation and CNA tables the filter icon only appears when:

there are samples that have not been profiled for a listed gene/mutation

there are more than one samples.

alisman · 2019-10-15T21:11:39Z

src/pages/patientView/PatientViewPageUtils.tsx

@@ -0,0 +1,19 @@
+import SampleManager from "./SampleManager";


seems like these first two imports are not used

Unused imports removed.

alisman · 2019-10-15T21:13:45Z

src/pages/patientView/PatientViewPageUtils.tsx

+                                            sampleToGenePanelId:{[sampleId:string]:string},
+                                            genePanelIdToEntrezGeneIds:{[genePanelId:string]:number[]}
+):boolean {
+    return !! _.find(entrezGeneIds, entrezGeneId => {


_.some is a little easier to read and returns boolean

Good point. Updated code.

alisman · 2019-11-04T15:18:45Z

src/pages/patientView/mutation/style.scss

@@ -0,0 +1,5 @@
+div.lazy-mobx-table {


why do we do this?

alisman · 2019-11-04T15:20:34Z

src/pages/patientView/PatientViewPage.tsx

@@ -226,6 +227,34 @@ export default class PatientViewPage extends React.Component<IPatientViewPagePro
        }
    });

+    @autobind


should be tagged @action since it mutates

alisman · 2019-11-04T15:20:42Z

src/pages/patientView/PatientViewPage.tsx

@@ -226,6 +227,34 @@ export default class PatientViewPage extends React.Component<IPatientViewPagePro
        }
    });

+    @autobind
+    private onFilterGenesMutationTable(option:GeneFilterOption):void {


alisman · 2019-11-04T15:20:51Z

src/pages/patientView/PatientViewPage.tsx

+    }
+
+    @autobind
+    private onFilterGenesCopyNumberTable(option:GeneFilterOption):void {


alisman · 2019-11-04T15:23:01Z

src/pages/patientView/clinicalInformation/PatientViewPageStore.ts

@@ -843,6 +853,24 @@ export class PatientViewPageStore {
        return mergeMutationsIncludingUncalled(this.mutationData, this.uncalledMutationData);
    }

+    @computed get mergedMutationDataIncludingUncalledFilteredByGene():Mutation[][] {
+        if (this.mutationTableGeneFilterOption === GeneFilterOption.ALL_SAMPLES) {


could use a comment

pvannierop added feature hyve RFC45 PatientView: gene panel integration labels Sep 19, 2019

pvannierop self-assigned this Sep 19, 2019

pvannierop changed the title ~~Patientview gene coverage filter~~ Gene coverage filter in Patient View mutation and CNA tables Sep 19, 2019

pvannierop requested review from adamabeshouse, alisman and inodb September 19, 2019 10:15

pvannierop force-pushed the patientview_gene_coverage_filter branch from f2ded70 to a696a43 Compare September 19, 2019 10:29

pvannierop force-pushed the patientview_genepanel_table_integration branch from 9f519af to 900f8ef Compare September 19, 2019 12:20