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Add v2 RMC dataset #1216

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merged 7 commits into from
Oct 28, 2023
Merged

Add v2 RMC dataset #1216

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8267938
Render exons in regional missense constraint track
nawatts Nov 23, 2020
4122249
Adjust color scale for regional missense constraint
nawatts Nov 25, 2020
f1d718d
Move o/e labels outside exons in regional missense constraint track
rileyhgrant Feb 10, 2023
116f5af
Add legend to regional missense constraint track
rileyhgrant Feb 10, 2023
0cf47dc
Add v2 regional missense constraint to Frontend
rileyhgrant Apr 3, 2023
37d99f7
Add v2 regional missense constraint to Data Pipeline
rileyhgrant Feb 9, 2023
fc4d41a
Add v2 regional missense constraint to GraphQL API
rileyhgrant Feb 9, 2023
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1 change: 1 addition & 0 deletions browser/cypress/fixtures/grch37_reference_stub.json
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Original file line number Diff line number Diff line change
Expand Up @@ -1342,6 +1342,7 @@
"flags": []
},
"exac_regional_missense_constraint_regions": null,
"gnomad_v2_regional_missense_constraint_regions": null,
"heterozygous_variant_cooccurrence_counts": [
{
"csq": "lof_lof",
Expand Down
10 changes: 10 additions & 0 deletions browser/src/GenePage/GenePage.tsx
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Expand Up @@ -19,6 +19,7 @@ import {
ReferenceGenome,
hasExons,
isExac,
isV2,
} from '@gnomad/dataset-metadata/metadata'
import ConstraintTable from '../ConstraintTable/ConstraintTable'
import VariantCooccurrenceCountsTable, {
Expand All @@ -31,6 +32,7 @@ import GnomadPageHeading from '../GnomadPageHeading'
import InfoButton from '../help/InfoButton'
import Link from '../Link'
import RegionalConstraintTrack from '../RegionalConstraintTrack'
import RegionalMissenseConstraintTrack, { RegionalMissenseConstraint} from '../RegionalMissenseConstraintTrack'
import RegionCoverageTrack from '../RegionPage/RegionCoverageTrack'
import RegionViewer from '../RegionViewer/ZoomableRegionViewer'
import { TrackPage, TrackPageSection } from '../TrackPage'
Expand Down Expand Up @@ -106,6 +108,7 @@ export type Gene = GeneMetadata & {
id: string
}[]
exac_regional_missense_constraint_regions?: any
gnomad_v2_regional_missense_constraint?: RegionalMissenseConstraint
variants: Variant[]
structural_variants: StructuralVariant[]
clinvar_variants: ClinvarVariant[]
Expand Down Expand Up @@ -568,6 +571,13 @@ const GenePage = ({ datasetId, gene, geneId }: Props) => {
/>
)}

{isV2(datasetId) && (
<RegionalMissenseConstraintTrack
regionalMissenseConstraint={gene.gnomad_v2_regional_missense_constraint}
gene={gene}
/>
)}

{/* eslint-disable-next-line no-nested-ternary */}
{hasStructuralVariants(datasetId) ? (
<StructuralVariantsInGene datasetId={datasetId} gene={gene} zoomRegion={zoomRegion} />
Expand Down
16 changes: 16 additions & 0 deletions browser/src/GenePage/GenePageContainer.tsx
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Expand Up @@ -224,6 +224,22 @@ query ${operationName}($geneId: String, $geneSymbol: String, $referenceGenome: R
obs_exp
chisq_diff_null
}
gnomad_v2_regional_missense_constraint {
passed_qc
has_no_rmc_evidence
regions {
chrom
start
stop
aa_start
aa_stop
obs_mis
exp_mis
obs_exp
chisq_diff_null
p_value
}
}
short_tandem_repeats(dataset: $shortTandemRepeatDatasetId) @include(if: $includeShortTandemRepeats) {
id
}
Expand Down
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