Skip to content

Commit

Permalink
fix(browser): render single source values in freq table
Browse files Browse the repository at this point in the history
  • Loading branch information
@rileyhgrant
rileyhgrant committed Oct 30, 2024
1 parent cb1846f commit 0204c30
Show file tree
Hide file tree
Showing 3 changed files with 184 additions and 4 deletions.
1 change: 1 addition & 0 deletions browser/src/VariantList/Variants.tsx
View file
Original file line number Diff line number Diff line change
Expand Up @@ -164,6 +164,7 @@ const Variants = ({
return mergeExomeAndGenomeData({
datasetId,
variants: filterVariants(variants, filter, renderedTableColumns),
preferJointData: filter.includeExomes && filter.includeGenomes,
})
}, [datasetId, variants, filter, renderedTableColumns])

Expand Down
183 changes: 180 additions & 3 deletions browser/src/VariantList/mergeExomeAndGenomeData.spec.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -370,6 +370,7 @@ describe('mergeExomeAndGenomeData', () => {

expect(result).toStrictEqual(expected)
})

it('returns just genome populations if only genome data is present, but no dataset', () => {
const genomeGeneticAncestryGroupObjects = createAncestryGroupObjects(
[
Expand Down Expand Up @@ -487,6 +488,7 @@ describe('mergeExomeAndGenomeData', () => {

expect(result).toStrictEqual(expected)
})

it('preferentially uses joint populations if both exome and joint are present, but no dataset', () => {
const exomeGeneticAncestryGroupObjects = createAncestryGroupObjects(
[
Expand Down Expand Up @@ -533,7 +535,13 @@ describe('mergeExomeAndGenomeData', () => {
},
})

const result = mergeExomeAndGenomeData({ variants: [testExomeAndJointVariant] })
const includeExomes = true
const includeGenomes = true

const result = mergeExomeAndGenomeData({
variants: [testExomeAndJointVariant],
preferJointData: includeExomes && includeGenomes,
})

const expectedJointGeneticAncestryGroupObjects = createAncestryGroupObjects(
[
Expand Down Expand Up @@ -561,6 +569,84 @@ describe('mergeExomeAndGenomeData', () => {

expect(result).toStrictEqual(expected)
})

it('Falls back to exome populations if both exome and joint are present, but user toggled off genome', () => {
const exomeGeneticAncestryGroupObjects = [
{ ac: 1, ac_hemi: 2, ac_hom: 3, an: 10, id: 'afr' },
{ ac: 2, ac_hemi: 3, ac_hom: 4, an: 20, id: 'remaining' },
{ ac: 4, ac_hemi: 5, ac_hom: 6, an: 40, id: 'eur' },
]

const jointGeneticAncestryGroupObjects = [
{ ac: 1, hemizygote_count: 2, homozygote_count: 3, an: 10, id: 'afr' },
{ ac: 2, hemizygote_count: 3, homozygote_count: 4, an: 20, id: 'remaining' },
{ ac: 3, hemizygote_count: 4, homozygote_count: 5, an: 30, id: 'eur' },
{ ac: 4, hemizygote_count: 5, homozygote_count: 6, an: 40, id: 'mid' },
]

const testExomeAndJointVariant = variantFactory.build({
variant_id: 'test_variant',
exome: {
ac: 1,
ac_hemi: 2,
ac_hom: 3,
faf95: {
popmax: null,
popmax_population: null,
},
an: 4,
af: 5,
filters: ['RF'],
populations: exomeGeneticAncestryGroupObjects as Population[],
},
joint: {
ac: 10,
hemizygote_count: 20,
homozygote_count: 30,
faf95: {
popmax: null,
popmax_population: null,
},
an: 40,
filters: ['discrepant_frequencies'],
populations: jointGeneticAncestryGroupObjects as Population[],
},
})

const includeExomes = true
const includeGenomes = false

const result = mergeExomeAndGenomeData({
variants: [testExomeAndJointVariant],
preferJointData: includeExomes && includeGenomes,
})

const expectedJointGeneticAncestryGroupObjects = createAncestryGroupObjects(
[
{ id: 'afr', value: 1 },
{ id: 'remaining', value: 2 },
{ id: 'eur', value: 4 },
],
false
)

const expected = [
{
...testExomeAndJointVariant,
ac: 1,
ac_hemi: 2,
ac_hom: 3,
an: 4,
af: 0.25,
allele_freq: 0.25,
filters: ['RF'],
populations: expectedJointGeneticAncestryGroupObjects,
},
]

expect(result).toStrictEqual(expected)
})

it('preferentially uses joint populations if both genome and joint are present, but no dataset', () => {
const genomeGeneticAncestryGroupObjects = createAncestryGroupObjects(
[
Expand Down Expand Up @@ -607,7 +693,13 @@ describe('mergeExomeAndGenomeData', () => {
},
})

const result = mergeExomeAndGenomeData({ variants: [testGenomeAndJointVariant] })
const includeExomes = true
const includeGenomes = true

const result = mergeExomeAndGenomeData({
variants: [testGenomeAndJointVariant],
preferJointData: includeExomes && includeGenomes,
})

const expectedJointGeneticAncestryGroupObjects = createAncestryGroupObjects(
[
Expand All @@ -634,6 +726,85 @@ describe('mergeExomeAndGenomeData', () => {

expect(result).toStrictEqual(expected)
})

it('Falls back to genome frequencies if both genome and joint are present, but user toggled off exome', () => {
const genomeGeneticAncestryGroupObjects = [
{ ac: 8, ac_hemi: 9, ac_hom: 10, an: 80, id: 'afr' },
{ ac: 16, ac_hemi: 17, ac_hom: 18, an: 160, id: 'remaining' },
{ ac: 32, ac_hemi: 33, ac_hom: 34, an: 320, id: 'eur' },
{ ac: 64, ac_hemi: 65, ac_hom: 66, an: 640, id: 'mid' },
]

const jointGeneticAncestryGroupObjects = [
{ ac: 1, hemizygote_count: 2, homozygote_count: 3, an: 10, id: 'afr' },
{ ac: 2, hemizygote_count: 3, homozygote_count: 4, an: 20, id: 'remaining' },
{ ac: 4, hemizygote_count: 5, homozygote_count: 6, an: 40, id: 'eur' },
]

const testGenomeAndJointVariant = variantFactory.build({
variant_id: 'test_variant',
genome: {
ac: 1,
ac_hemi: 2,
ac_hom: 3,
faf95: {
popmax: null,
popmax_population: null,
},
an: 4,
af: 5,
filters: ['RF'],
populations: genomeGeneticAncestryGroupObjects as Population[],
},
joint: {
ac: 10,
hemizygote_count: 20,
homozygote_count: 30,
faf95: {
popmax: null,
popmax_population: null,
},
an: 40,
filters: ['discrepant_frequencies'],
populations: jointGeneticAncestryGroupObjects as Population[],
},
})

const includeExomes = false
const includeGenomes = true

const result = mergeExomeAndGenomeData({
variants: [testGenomeAndJointVariant],
preferJointData: includeExomes && includeGenomes,
})

const expectedGenomeGeneticAncestryGroupObjects = createAncestryGroupObjects(
[
{ id: 'afr', value: 8 },
{ id: 'remaining', value: 16 },
{ id: 'eur', value: 32 },
{ id: 'mid', value: 64 },
],
false
)

const expected = [
{
...testGenomeAndJointVariant,
ac: 1,
ac_hemi: 2,
ac_hom: 3,
an: 4,
af: 0.25,
allele_freq: 0.25,
filters: ['RF'],
populations: expectedGenomeGeneticAncestryGroupObjects,
},
]

expect(result).toStrictEqual(expected)
})

it('preferentially uses joint populations if exome, genome and joint are present, but no dataset', () => {
const exomeGeneticAncestryGroupObjects = createAncestryGroupObjects(
[
Expand Down Expand Up @@ -703,7 +874,13 @@ describe('mergeExomeAndGenomeData', () => {
},
})

const result = mergeExomeAndGenomeData({ variants: [testExomeGenomeAndJointVariant] })
const includeExomes = true
const includeGenomes = true

const result = mergeExomeAndGenomeData({
variants: [testExomeGenomeAndJointVariant],
preferJointData: includeExomes && includeGenomes,
})

const expectedJointGeneticAncestryGroupObjects = createAncestryGroupObjects(
[
Expand Down
4 changes: 3 additions & 1 deletion browser/src/VariantList/mergeExomeAndGenomeData.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -125,14 +125,16 @@ type MergedVariant = Variant & {
export const mergeExomeAndGenomeData = ({
datasetId,
variants,
preferJointData = false,
}: {
datasetId?: DatasetId
variants: Variant[]
preferJointData?: boolean
}): MergedVariant[] => {
const mergedVariants = variants.map((variant: Variant) => {
const { exome, genome, joint } = variant

if (joint) {
if (joint && preferJointData) {
const exomeFilters = exome ? exome.filters : []
const genomeFilters = genome ? genome.filters : []
const jointFilters = exomeFilters.concat(genomeFilters, joint.filters)
Expand Down

0 comments on commit 0204c30

Please sign in to comment.