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TASK-4451 - Variant and Sample Variant Browser discrepancies and other visualisation details to fix #900

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merged 8 commits into from
May 16, 2024
Merged

TASK-4451 - Variant and Sample Variant Browser discrepancies and other visualisation details to fix #900

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a89145e
wc: fix pop freqs issues
imedina Jun 12, 2023
dc226b2
wc: minor fixes in the the cellbase grid
imedina Jun 12, 2023
d0b7ff7
Fix cohort-stats rounded freqs
imedina Apr 4, 2024
efe847a
Merge branch 'release-2.8.x' into TASK-4451
imedina Apr 4, 2024
40be6ca
Merge branch 'release-2.12.x' into TASK-4451
imedina Apr 4, 2024
f869daa
Merge branch 'release-2.12.x' into TASK-4451
jmjuanes Apr 24, 2024
8c705e3
Merge branch 'release-2.12.x' into TASK-4451
jmjuanes Apr 30, 2024
4615c01
Merge branch 'release-2.12.x' into TASK-4451
jmjuanes May 16, 2024
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8 changes: 7 additions & 1 deletion src/sites/iva/conf/config.js
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ const hosts = [
url: "https://ws.opencb.org/opencga-prod"
},
{
id: "test1",
id: "demo",
url: "https://demo.app.zettagenomics.com/opencga"
},
{
Expand Down Expand Up @@ -194,6 +194,12 @@ const SUITE = {
{id: "getting-started", name: "Getting Started", tab: false, url: "#getting-started", icon: "fa fa-book"}
]
},
jobMonitor: {
visibility: "private"
},
fileExplorer: {
visibility: "private"
},
restApi: {
visibility: "private"
},
Expand Down
61 changes: 35 additions & 26 deletions src/webcomponents/variant/annotation/cellbase-population-frequency-grid.js
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ export default class CellbasePopulationFrequencyGrid extends LitElement {
constructor() {
super();

this._init();
this.#init();
}

createRenderRoot() {
Expand All @@ -50,7 +50,7 @@ export default class CellbasePopulationFrequencyGrid extends LitElement {
};
}

_init() {
#init() {
this._prefix = UtilsNew.randomString(8);

this.populationFrequencies = [];
Expand All @@ -76,15 +76,12 @@ export default class CellbasePopulationFrequencyGrid extends LitElement {
}

variantIdObserver() {
console.log("variantIdObserver", this.variantId, this.cellbaseClient);
if (this.cellbaseClient && this.variantId) {
this.cellbaseClient.get("genomic", "variant", this.variantId, "annotation", {assembly: this.assembly}, {})
.then(restResponse => {
this.populationFrequencies = restResponse.getResult(0).populationFrequencies;
this.requestUpdate();
});
} else {
// this.populationFrequencies = null;
}
}

Expand All @@ -94,17 +91,20 @@ export default class CellbasePopulationFrequencyGrid extends LitElement {
return refAllele + "/" + altAllele;
}

freqFormatter(value, row, index) {
return (value !== 0 && value !== 1) ? Number(value).toFixed(4) : value;
freqFormatter(value, count) {
if (typeof value === "undefined") {
return "NA";
}
return (value !== 0 && value !== 1) ? `<span style="margin:0 5px">${Number(value).toPrecision(4)}</span> / <span style="margin:0 5px">${count}</span> (${(value * 100).toPrecision(4)} %)` : value;
}

renderPlot() {
const popArray = [];
const mafArray = [];
if (typeof this.populationFrequencies !== "undefined") {
if (this.populationFrequencies) {
for (let i = 0; i < this.populationFrequencies.length; i++) {
popArray.push(this.populationFrequencies[i].study + "-" + this.populationFrequencies[i].population);
mafArray.push(Math.min(Number(this.populationFrequencies[i].refAlleleFreq).toFixed(4), Number(this.populationFrequencies[i].altAlleleFreq).toFixed(4)));
mafArray.push(Math.min(Number(this.populationFrequencies[i].refAlleleFreq).toPrecision(4), Number(this.populationFrequencies[i].altAlleleFreq).toPrecision(4)));
}
}

Expand Down Expand Up @@ -203,14 +203,28 @@ export default class CellbasePopulationFrequencyGrid extends LitElement {
colspan: 1
},
{
title: "Allele Frequency",
title: "Number of Samples",
rowspan: 2,
colspan: 1,
formatter: (value, row) => {
if (row.refHomGenotypeCount || row.hetGenotypeCount || row.altHomGenotypeCount) {
return row.refHomGenotypeCount + row.hetGenotypeCount + row.altHomGenotypeCount;
} else {
return (row?.refAlleleCount + row?.altAlleleCount) / 2;
}
},
halign: "center",
align: "right"
},
{
title: "Allele Info",
rowspan: 1,
colspan: 2,
formatter: this.alleleFormatter,
halign: "center"
},
{
title: "Genotype Frequency",
title: "Genotype Info",
rowspan: 1,
colspan: 3,
formatter: this.alleleFormatter,
Expand All @@ -219,52 +233,47 @@ export default class CellbasePopulationFrequencyGrid extends LitElement {
],
[
{
title: "Reference",
field: "refAlleleFreq",
title: `Reference Allele<br><span style="font-style: italic">Freq / Count (%)</span>`,
rowspan: 1,
colspan: 1,
sortable: true,
formatter: this.freqFormatter,
formatter: (value, row) => this.freqFormatter(row.refAlleleFreq, row.refAlleleCount),
halign: "center",
align: "right"
},
{
title: "Alternate",
field: "altAlleleFreq",
title: `Alternate Allele<br><span style="font-style: italic">Freq / Count (%)</span>`,
rowspan: 1,
colspan: 1,
sortable: true,
formatter: this.freqFormatter,
formatter: (value, row) => this.freqFormatter(row.altAlleleFreq, row.altAlleleCount),
halign: "center",
align: "right"
},
{
title: "Ref/Ref",
field: "refHomGenotypeFreq",
title: `Ref/Ref Genotype<br><span style="font-style: italic">Freq / Count (%)</span>`,
rowspan: 1,
colspan: 1,
sortable: true,
formatter: this.freqFormatter,
formatter: (value, row) => this.freqFormatter(row.refHomGenotypeFreq, row.refHomGenotypeCount),
halign: "center",
align: "right"
},
{
title: "Ref/Alt",
field: "hetGenotypeFreq",
title: `Ref/Alt Genotype<br><span style="font-style: italic">Freq / Count (%)</span>`,
rowspan: 1,
colspan: 1,
sortable: true,
formatter: this.freqFormatter,
formatter: (value, row) => this.freqFormatter(row.hetGenotypeFreq, row.hetGenotypeCount),
halign: "center",
align: "right"
},
{
title: "Alt/Alt",
field: "altHomGenotypeFreq",
title: `Alt/Alt Genotype<br><span style="font-style: italic">Freq / Count (%)</span>`,
rowspan: 1,
colspan: 1,
sortable: true,
formatter: this.freqFormatter,
formatter: (value, row) => this.freqFormatter(row.altHomGenotypeFreq, row.altHomGenotypeCount),
halign: "center",
align: "right"
}
Expand Down
17 changes: 8 additions & 9 deletions src/webcomponents/variant/interpretation/variant-interpreter-grid-formatter.js
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Original file line number Diff line number Diff line change
Expand Up @@ -92,20 +92,19 @@ export default class VariantInterpreterGridFormatter {
}

static clinicalPopulationFrequenciesFormatter(value, row) {
const popFreqMap = new Map();
// If variant population freqs exist read values
if (row?.annotation?.populationFrequencies?.length > 0) {
const popFreqMap = new Map();
row.annotation.populationFrequencies.forEach(popFreq => {
popFreqMap.set(popFreq.study + ":" + popFreq.population, popFreq);
});
return VariantGridFormatter.renderPopulationFrequencies(
this._config.populationFrequencies,
popFreqMap,
POPULATION_FREQUENCIES.style,
this._config.populationFrequenciesConfig,
);
} else {
return "-";
}
return VariantGridFormatter.renderPopulationFrequencies(
this._config.populationFrequencies,
popFreqMap,
POPULATION_FREQUENCIES.style,
this._config.populationFrequenciesConfig,
);
}

static predictionFormatter(value, row) {
Expand Down
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