,
}
];
diff --git a/src/components/orthology/index.js b/src/components/orthology/index.js
index 52e834d71..ea5eb54b0 100644
--- a/src/components/orthology/index.js
+++ b/src/components/orthology/index.js
@@ -3,6 +3,8 @@ import OrthologyFilteredTable from './orthologyFilteredTable';
import HomologyUserGuide from '../homology/homologyUserGuide';
import OrthologyBasicInfo from './orthologyBasicInfo';
import StringencySelection from '../homology/stringencySelection';
+import OrthologyJBrowseLink from './orthologyJBrowseLink';
+import OrthologyJBrowseLinkPanel from './orthologyJBrowseLinkPanel';
export {
OrthologyBasicInfo,
@@ -10,6 +12,8 @@ export {
OrthologyFilteredTable,
HomologyUserGuide,
StringencySelection,
+ OrthologyJBrowseLink,
+ OrthologyJBrowseLinkPanel
};
export * from '../homology/utils';
diff --git a/src/components/orthology/orthologyJBrowseLink.js b/src/components/orthology/orthologyJBrowseLink.js
new file mode 100644
index 000000000..ac1e1cd29
--- /dev/null
+++ b/src/components/orthology/orthologyJBrowseLink.js
@@ -0,0 +1,57 @@
+import React from 'react';
+import PropTypes from 'prop-types';
+import {stringify as stringifyQuery} from 'qs';
+import ExternalLink from '../ExternalLink';
+import {
+ getSpecies
+} from '../../lib/utils';
+
+const buildTrackList = (taxonid,filterlevel) => {
+ const trackList = getSpecies(taxonid).jBrowseOrthologyTracks.replace(/filter/g, filterlevel);
+ return trackList;
+};
+
+const buildAssembly = (taxonid) => {
+ return getSpecies(taxonid).jBrowseName.replace(' ', '_');
+}
+
+const buildLocation = (geneLocation, taxonid) => {
+ const chrom = (taxonid === 'NCBITaxon:559292' || (taxonid === 'NCBITaxon:8355' && !(geneLocation.chromosome.startsWith('Scaffold')) ) )
+ ? 'chr' + geneLocation.chromosome : geneLocation.chromosome;
+ return chrom + ':' + geneLocation.start + '..' + geneLocation.end;
+}
+
+const buildAnchor = (filterlevel) => {
+ return filterlevel === 'none' ? 'No filter'
+ : filterlevel === 'best' ? 'Best and Best Reverse'
+ : filterlevel === 'moderate' ? 'Moderate'
+ : filterlevel === 'stringent' ? 'Stringent' : '';
+}
+
+const OrthologyJBrowseLink = ({filterlevel, geneLocation, taxonid}) => {
+ return (
+
+ {buildAnchor(filterlevel)}
+
+ );
+};
+
+OrthologyJBrowseLink.propTypes = {
+ children: PropTypes.node,
+ geneLocation: PropTypes.shape({
+ start: PropTypes.number,
+ end: PropTypes.number,
+ chromosome: PropTypes.string,
+ }),
+ taxonid: PropTypes.string.isRequired,
+ filterlevel: PropTypes.string.isRequired
+};
+
+export default OrthologyJBrowseLink;
diff --git a/src/components/orthology/orthologyJBrowseLinkPanel.js b/src/components/orthology/orthologyJBrowseLinkPanel.js
new file mode 100644
index 000000000..3285a0d15
--- /dev/null
+++ b/src/components/orthology/orthologyJBrowseLinkPanel.js
@@ -0,0 +1,57 @@
+import React from 'react';
+import PropTypes from 'prop-types';
+import OrthologyJBrowseLink from './orthologyJBrowseLink';
+
+const geneLocationIsInvalid = (geneLocation) => {
+ if (typeof geneLocation.chromosome === 'undefined') {
+ return true;
+ } else if (typeof geneLocation.start === 'undefined') {
+ return true;
+ } else if (typeof geneLocation.end === 'undefined') {
+ return true;
+ }
+ return false;
+}
+
+const OrthologyJBrowseLinkPanel = ({geneLocation, taxonid}) => {
+ return (
+ (geneLocationIsInvalid(geneLocation) || taxonid === 'NCBITaxon:2697049') ? null :
+
+ Links to orthology data in JBrowse by filter level:
+
+ ,
+
+ ,
+
+ ,
+
+
+ );
+};
+
+OrthologyJBrowseLinkPanel.propTypes = {
+ geneLocation: PropTypes.shape({
+ start: PropTypes.number,
+ end: PropTypes.number,
+ chromosome: PropTypes.string,
+ }),
+ taxonid: PropTypes.string.isRequired
+};
+
+export default OrthologyJBrowseLinkPanel;
diff --git a/src/components/pathway/pathwayWidget.js b/src/components/pathway/pathwayWidget.js
index a3c8018fb..03fa96f77 100644
--- a/src/components/pathway/pathwayWidget.js
+++ b/src/components/pathway/pathwayWidget.js
@@ -482,18 +482,10 @@ class PathwayWidget extends Component {
-
+ show-legend="true"
+ style={{ "maxWidth": "1280px" }}>
+
:
diff --git a/src/components/variant/VariantJBrowseLink.js b/src/components/variant/VariantJBrowseLink.js
index eabb97788..cee8a2e10 100644
--- a/src/components/variant/VariantJBrowseLink.js
+++ b/src/components/variant/VariantJBrowseLink.js
@@ -2,7 +2,11 @@ import React from 'react';
import PropTypes from 'prop-types';
import {stringify as stringifyQuery} from 'qs';
import ExternalLink from '../ExternalLink';
+import {
+ getSpecies
+} from '../../lib/utils';
+// this will return when the get parameter 'highlight' is added to JB2
const calculateHighlight = (location, type) => {
switch(type){
case 'insertion':
@@ -16,16 +20,42 @@ const calculateHighlight = (location, type) => {
}
};
-const VariantJBrowseLink = ({children, location, type, geneSymbol, geneLocation, species}) => {
+const LINK_BUFFER = 1.2;
+
+const buildTrackList = (taxonid) => {
+ const tracks = [];
+ const trackList = getSpecies(taxonid).jBrowsetracks.split(',');
+ const assembly = buildAssembly(taxonid);
+ for (const track of trackList) {
+ tracks.push( assembly + track );
+ }
+ return tracks.join(',');
+};
+
+const buildAssembly = (taxonid) => {
+ return getSpecies(taxonid).jBrowseName.replace(' ', '_');
+}
+
+const buildLoc = (location) => {
+ const start = location.start || 0;
+ const end = location.end || 0
+ const linkLength = end - start;
+ if (linkLength === 0 ) { return; }
+ let bufferedMin = Math.round(start - (linkLength * LINK_BUFFER / 2.5));
+ bufferedMin = bufferedMin < 0 ? 0 : bufferedMin;
+ const bufferedMax = Math.round(end + (linkLength * LINK_BUFFER ));
+ return location.chromosome + ':' + bufferedMin + '..' + bufferedMax ;
+}
+
+const VariantJBrowseLink = ({children, location, type, geneSymbol, geneLocation, taxonid}) => {
return (
location ?
@@ -47,8 +77,8 @@ VariantJBrowseLink.propTypes = {
end: PropTypes.number,
chromosome: PropTypes.string,
}),
- species: PropTypes.string.isRequired,
- type: PropTypes.string
+ type: PropTypes.string,
+ taxonid: PropTypes.string.isRequired
};
export default VariantJBrowseLink;
diff --git a/src/constants.js b/src/constants.js
index 395baf844..d3bf9c93e 100644
--- a/src/constants.js
+++ b/src/constants.js
@@ -89,8 +89,8 @@ export const NAV_MENU = [
external: true,
},
{
- label: 'JBrowse',
- route: '/jbrowse/?data=data%2FHomo%20sapiens',
+ label: 'JBrowse 2',
+ route: '/jbrowse2/',
external: true,
},
{
@@ -264,6 +264,8 @@ export const SPECIES = [
jBrowsenclistbaseurl: `https://s3.amazonaws.com/agrjbrowse/docker/${RELEASE}/human/`,
jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz',
jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001405.40_GRCh38.p14_genomic.fna.gz',
+ jBrowsetracks: '_all_genes,_ht_variants',
+ jBrowseOrthologyTracks: 'Homo_sapiens_all_genes,human2fly.filter.anchors,human2mouse.filter.anchors,human2rat.filter.anchors,human2worm.filter.anchors,human2xenopuslaevis.filter.anchors,human2xenopustropicalis.filter.anchors,human2yeast.filter.anchors,human2zebrafish.filter.anchors',
vertebrate: true,
enableSingleCellExpressionAtlasLink: true,
enableOrthologComparison: true,
@@ -278,6 +280,8 @@ export const SPECIES = [
jBrowsenclistbaseurl: `https://s3.amazonaws.com/agrjbrowse/docker/${RELEASE}/MGI/mouse/`,
jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz',
jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001635.27_GRCm39_genomic.fna.gz',
+ jBrowsetracks: '_all_genes,_ht_variants,_variants,_multiple-variant_alleles',
+ jBrowseOrthologyTracks:'Mus_musculus_all_genes,human2mouse.filter.anchors,mouse2fly.filter.anchors,mouse2worm.filter.anchors,mouse2xenopustropicalis.filter.anchors,mouse2yeast.filter.anchors,mouse2zebrafish.filter.anchors,rat2mouse.filter.anchors',
vertebrate: true,
enableSingleCellExpressionAtlasLink: true,
enableOrthologComparison: true,
@@ -292,6 +296,8 @@ export const SPECIES = [
jBrowsenclistbaseurl: `https://s3.amazonaws.com/agrjbrowse/docker/${RELEASE}/RGD/rat/`,
jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz',
jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_015227675.2_mRatBN7.2_genomic.fna.gz',
+ jBrowsetracks: '_all_genes,_ht_variants,_variants',
+ jBrowseOrthologyTracks:'Rattus_norvegicus_all_genes,human2rat.filter.anchors,rat2fly.filter.anchors,rat2mouse.filter.anchors,rat2worm.filter.anchors,rat2xenopustropicalis.filter.anchors,rat2yeast.filter.anchors,rat2zebrafish.filter.anchors',
vertebrate: true,
enableSingleCellExpressionAtlasLink: true,
enableOrthologComparison: true,
@@ -306,6 +312,8 @@ export const SPECIES = [
jBrowsenclistbaseurl: `https://s3.amazonaws.com/agrjbrowse/docker/${RELEASE}/XenBase/x_laevis/`,
jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz',
jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/XENLA_9.2_genome.fa.gz',
+ jBrowsetracks: '_all_genes',
+ jBrowseOrthologyTracks:'Xenopus_laevis_all_genes,human2xenopuslaevis.filter.anchors,xenopuslaevis2xenopustropicalis.filter.anchors',
vertebrate: true,
enableSingleCellExpressionAtlasLink: false,
enableOrthologComparison: true,
@@ -320,6 +328,8 @@ export const SPECIES = [
jBrowsenclistbaseurl: `https://s3.amazonaws.com/agrjbrowse/docker/${RELEASE}/XenBase/x_tropicalis/`,
jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz',
jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/XENTR_9.1_genome.fa.gz',
+ jBrowsetracks: '_all_genes',
+ jBrowseOrthologyTracks:'Xenopus_tropicalis_all_genes,human2xenopustropicalis.filter.anchors,mouse2xenopustropicalis.filter.anchors,rat2xenopustropicalis.filter.anchors,xenopuslaevis2xenopustropicalis.filter.anchors,xenopustropicalis2fly.filter.anchors,xenopustropicalis2worm.filter.anchors,xenopustropicalis2yeast.filter.anchors,zebrafish2xenopustropicalis.filter.anchors',
vertebrate: true,
enableSingleCellExpressionAtlasLink: false,
enableOrthologComparison: true,
@@ -334,6 +344,8 @@ export const SPECIES = [
jBrowsenclistbaseurl: `https://s3.amazonaws.com/agrjbrowse/docker/${RELEASE}/zfin/zebrafish-11/`,
jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz',
jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000002035.6_GRCz11_genomic.fna.gz',
+ jBrowsetracks: '_all_genes,_ht_variants,_variants',
+ jBrowseOrthologyTracks:'Danio_rerio_all_genes,human2zebrafish.filter.anchors,mouse2zebrafish.filter.anchors,rat2zebrafish.filter.anchors,zebrafish2fly.filter.anchors,zebrafish2worm.filter.anchors,zebrafish2xenopustropicalis.filter.anchors,zebrafish2yeast.filter.anchors',
vertebrate: true,
enableSingleCellExpressionAtlasLink: true,
enableOrthologComparison: true,
@@ -348,6 +360,8 @@ export const SPECIES = [
jBrowsenclistbaseurl: `https://s3.amazonaws.com/agrjbrowse/docker/${RELEASE}/FlyBase/fruitfly/`,
jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz',
jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.gz',
+ jBrowsetracks: '_all_genes,_ht_variants,_variants,_multiple-variant_alleles',
+ jBrowseOrthologyTracks:'Drosophila_melanogaster_all_genes,fly2yeast.filter.anchors,human2fly.filter.anchors,mouse2fly.filter.anchors,rat2fly.filter.anchors,worm2fly.filter.anchors,xenopustropicalis2fly.filter.anchors,zebrafish2fly.filter.anchors',
vertebrate: false,
enableSingleCellExpressionAtlasLink: true,
enableOrthologComparison: true,
@@ -362,6 +376,8 @@ export const SPECIES = [
jBrowsenclistbaseurl: `https://s3.amazonaws.com/agrjbrowse/docker/${RELEASE}/WormBase/c_elegans_PRJNA13758/`,
jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz',
jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000002985.6_WBcel235_genomic.fna.gz',
+ jBrowsetracks: '_all_genes,_ht_variants,_variants',
+ jBrowseOrthologyTracks:'Caenorhabditis_elegans_all_genes,human2worm.filter.anchors,mouse2worm.filter.anchors,rat2worm.filter.anchors,worm2fly.filter.anchors,worm2yeast.filter.anchors,xenopustropicalis2worm.filter.anchors,zebrafish2worm.filter.anchors',
vertebrate: false,
enableSingleCellExpressionAtlasLink: true,
enableOrthologComparison: true,
@@ -376,6 +392,8 @@ export const SPECIES = [
jBrowsenclistbaseurl: `https://s3.amazonaws.com/agrjbrowse/docker/${RELEASE}/SGD/yeast/`,
jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz',
jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000146045.2_R64_genomic.fna.gz',
+ jBrowsetracks: '_all_genes,_ht_variants',
+ jBrowseOrthologyTracks:'Saccharomyces_cerevisiae_all_genes,fly2yeast.filter.anchors,human2yeast.filter.anchors,mouse2yeast.filter.anchors,rat2yeast.filter.anchors,worm2yeast.filter.anchors,xenopustropicalis2yeast.filter.anchors,zebrafish2yeast.filter.anchors',
vertebrate: false,
enableSingleCellExpressionAtlasLink: true,
enableOrthologComparison: true,
@@ -390,6 +408,8 @@ export const SPECIES = [
jBrowsenclistbaseurl: `https://s3.amazonaws.com/agrjbrowse/docker/3.2.0/SARS-CoV-2/`,
jBrowseurltemplate: 'tracks/All Genes/{refseq}/trackData.jsonz',
jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001405.40_GRCh38.p14_genomic.fna.gz',
+ jBrowsetracks: '_all_genes',
+ jBrowseOrthologyTracks:'',
suppressFlatten: true,
vertebrate: false,
enableSingleCellExpressionAtlasLink: false,
@@ -416,3 +436,4 @@ export const GA_EVENT_ACTION = {
SET_PAGE_SIZE: 'Set page size'
};
+export const DOWNLOAD_BUTTON_THRESHOLD = 90000;
diff --git a/src/containers/GeneAlleleDetailsPage/GeneAlleleDetailsTable.js b/src/containers/GeneAlleleDetailsPage/GeneAlleleDetailsTable.js
index 5807bda66..a460cf4bc 100644
--- a/src/containers/GeneAlleleDetailsPage/GeneAlleleDetailsTable.js
+++ b/src/containers/GeneAlleleDetailsPage/GeneAlleleDetailsTable.js
@@ -120,6 +120,7 @@ const GeneAlleleDetailsTable = ({ isLoadingGene, gene, geneId }) => {
location={variant.location}
species={gene.species && gene.species.name}
type={variant.variantType && variant.variantType.name}
+ taxonid={gene.species && gene.species.taxonId}
>{variant.displayName}
) : null,
diff --git a/src/containers/allelePage/AlleleSequenceView.js b/src/containers/allelePage/AlleleSequenceView.js
index 06526553f..48194bc6c 100644
--- a/src/containers/allelePage/AlleleSequenceView.js
+++ b/src/containers/allelePage/AlleleSequenceView.js
@@ -22,6 +22,13 @@ function findFminFmax(genomeLocation, variants) {
return { fmin, fmax };
}
+function findAlleleStart(variants) {
+ if (variants && variants.data.results) {
+//just get the start of the first variant
+ return variants[0].data.results.location.start;
+ }
+}
+
const AlleleSequenceView = ({ allele }) => {
const variants = useAllAlleleVariants(allele.id);
const visibleTranscripts = useDataTableQuery(`/api/allele/${allele.id}/variants`);
@@ -41,8 +48,9 @@ const AlleleSequenceView = ({ allele }) => {
isoformFilter = visibleTranscripts.data[0].transcriptList.map(a => a.id.split(':').pop());
}
-
const { fmin, fmax } = findFminFmax(genomeLocation, variants);
+ //highjacking the htpVaraint to send the start of the variant itself
+ const htpVariant = findAlleleStart(variants);
return (
{
displayType='ISOFORM_AND_VARIANT'
fmax={fmax}
fmin={fmin}
+ htpVariant={htpVariant}
geneSymbol={allele.symbol}
genomeLocationList={genomeLocations}
height='200px'
diff --git a/src/containers/allelePage/AlleleToDiseaseTable.js b/src/containers/allelePage/AlleleToDiseaseTable.js
index 274893283..45bf1f014 100644
--- a/src/containers/allelePage/AlleleToDiseaseTable.js
+++ b/src/containers/allelePage/AlleleToDiseaseTable.js
@@ -53,7 +53,7 @@ const AlleleToDiseaseTable = ({alleleId}) => {
{
dataField: 'primaryAnnotations',
text: 'Annotation details',
- formatter: entities => ,
+ formatter: (entities, row) => ,
headerStyle: {width: '90px'},
},
{
@@ -71,9 +71,9 @@ const AlleleToDiseaseTable = ({alleleId}) => {
filterName: 'dataProvider',
},
{
- dataField: 'references',
+ dataField: 'pubmedPubModIDs',
text: 'References',
- formatter: references => ReferencesCellCuration(references),
+ formatter: (pubModIds) => ,
headerStyle: {width: '150px'},
filterable: true,
filterName: 'reference',
diff --git a/src/containers/allelePage/AlleleToVariantTable.js b/src/containers/allelePage/AlleleToVariantTable.js
index 669d9fd25..e313f962e 100644
--- a/src/containers/allelePage/AlleleToVariantTable.js
+++ b/src/containers/allelePage/AlleleToVariantTable.js
@@ -32,6 +32,7 @@ const AlleleToVariantTable = ({allele = {}, alleleId}) => {
location={location}
species={species.name}
type={type.name}
+ taxonid={species.taxonId}
>
{name}
@@ -94,6 +95,7 @@ AlleleToVariantTable.propTypes = {
}),
species: PropTypes.shape({
name: PropTypes.string,
+ taxonid: PropTypes.string
})
}),
alleleId: PropTypes.any,
diff --git a/src/containers/allelePage/VariantEffectDetails.js b/src/containers/allelePage/VariantEffectDetails.js
index afb3d532f..4e6de8c03 100644
--- a/src/containers/allelePage/VariantEffectDetails.js
+++ b/src/containers/allelePage/VariantEffectDetails.js
@@ -63,6 +63,7 @@ const VariantEffectDetails = ({
location={variant.location}
species={variant.species && variant.species.name}
type={variant.variantType && variant.variantType.name}
+ taxonid={variant.species && variant.species.taxonId}
>
{variant.id}
on {transcript.name}
diff --git a/src/containers/allelePage/VariantSummary.js b/src/containers/allelePage/VariantSummary.js
index 0759cc7f3..70197e483 100644
--- a/src/containers/allelePage/VariantSummary.js
+++ b/src/containers/allelePage/VariantSummary.js
@@ -39,7 +39,7 @@ const VariantSummary = ({variant}) => {
} = variant || {};
const genomeLocation = getVariantGenomeLocation(variant);
-
+ console.log(species);
return (
<>
Symbol
@@ -51,6 +51,7 @@ const VariantSummary = ({variant}) => {
location={location}
species={species && species.name}
type={type && type.name}
+ taxonid={species && species.taxonId}
>
{symbol || displayName || variantId}
diff --git a/src/containers/diseasePage/DiseaseToGeneTable.js b/src/containers/diseasePage/DiseaseToGeneTable.js
index 72fbfee68..3c982f387 100644
--- a/src/containers/diseasePage/DiseaseToGeneTable.js
+++ b/src/containers/diseasePage/DiseaseToGeneTable.js
@@ -1,113 +1,159 @@
import React from 'react';
import PropTypes from 'prop-types';
import {
- EvidenceCodesCell,
- GeneCell,
- ReferenceCell,
- SpeciesCell,
+ BasedOnGeneCellCuration,
DataTable,
- BasedOnGeneCell
+ EvidenceCodesCellCuration,
+ GeneCellCuration,
+ ReferencesCellCuration,
} from '../../components/dataTable';
-import {
- compareByFixedOrder,
-} from '../../lib/utils';
-import AnnotatedEntitiesPopup
- from '../../components/dataTable/AnnotatedEntitiesPopup';
-import DiseaseLink from '../../components/disease/DiseaseLink';
-import {getDistinctFieldValue} from '../../components/dataTable/utils';
-import {SPECIES_NAME_ORDER} from '../../constants';
-import ProvidersCell from '../../components/dataTable/ProvidersCell';
+
+import ProvidersCellCuration from '../../components/dataTable/ProvidersCellCuration';
import useDataTableQuery from '../../hooks/useDataTableQuery';
-import SpeciesName from '../../components/SpeciesName';
import AssociationType from '../../components/AssociationType';
+import { buildProvidersWithUrl, getIsViaOrthology, getDistinctFieldValue, getIdentifier } from '../../components/dataTable/utils';
+import { compareByFixedOrder } from '../../lib/utils';
+import { SPECIES_NAME_ORDER } from '../../constants';
+import SpeciesCell from '../../components/dataTable/SpeciesCell';
+import SpeciesName from '../../components/SpeciesName';
+import DiseaseLinkCuration from '../../components/disease/DiseaseLinkCuration';
+import DiseaseQualifiersColumn from '../../components/dataTable/DiseaseQualifiersColumn';
+import AnnotatedEntitiesPopupCuration from '../../components/dataTable/AnnotatedEntitiesPopupCuration';
+import ReferenceCellViaOrthologyCuration from '../../components/dataTable/ReferencesCellViaOrthologyCuration';
-const DiseaseToGeneTable = ({id}) => {
+const DiseaseToGeneTable = ({ id }) => {
const {
data: results,
resolvedData,
...tableProps
} = useDataTableQuery(`/api/disease/${id}/genes`, undefined, { sizePerPage: 10, }, {}, 60000);
+
+
const columns = [
{
- dataField: 'gene',
+ dataField: 'subject',
text: 'Gene',
- formatter: (gene, row) => (
-
- {GeneCell(gene)}
-
-
- Annotation details
-
-
-
- ),
+ formatter: (subject, row) => {
+ const isViaOrthology = getIsViaOrthology(row);
+ return (
+
+
+
+
+ {!isViaOrthology && (
+
+
+ Annotation details
+
+
+ )}
+
+ );
+ },
+ headerStyle: { width: '75px' },
filterable: true,
filterName: 'geneName',
- headerStyle: {width: '120px'},
},
{
- dataField: 'species',
+ dataField: 'subject.taxon',
text: 'Species',
- formatter: species => ,
+ headerStyle: { width: '100px' },
+ formatter: species => ,
+ filterName: 'species',
filterable: getDistinctFieldValue(resolvedData, 'species').sort(compareByFixedOrder(SPECIES_NAME_ORDER)),
filterFormatter: speciesName => {speciesName},
- headerStyle: {width: '105px'},
+ filterType: 'checkbox',
},
{
- dataField: 'associationType',
+ dataField: 'generatedRelationString',
text: 'Association',
+ helpPopupProps: {
+ id: 'disease-page--gene-disease-associations-table--association-help',
+ children:
+
"Is Implicated in" means that some variant of the gene is shown to function in causing or modifying a disease (for human) or a disease model state.
+
"Is a marker for" is used when there is evidence of an association but insufficient evidence to establish causality and does not necessarily imply that the existence of, or change in the biomarker is causal for the disease, but rather may result from it.
+
- Date: { isError ? 'Unknown' : new Date(releaseDate).toDateString()}
+ Date: { isError ? 'Unknown' : new Date(snapShotDate).toDateString()}
);
};
diff --git a/src/style.scss b/src/style.scss
index bb549479e..8ba9902ed 100644
--- a/src/style.scss
+++ b/src/style.scss
@@ -124,4 +124,48 @@ wc-ribbon-cell.ribbon__subject--cell--no-annotation {
--gocam-panel-process-font-weight: 400;
--gocam-panel-h1-color: #2598C5;
--gocam-panel-h1-weight: 400;
+}
+
+wc-gocam-viz {
+ --activity-background-active: #af732a;
+ --activity-color-active: #fff;
+ --button-background: #DDD;
+ --button-color: #000;
+ --button-background-hover: #BBB;
+ --button-border-width: 1px;
+ --button-border-color: #ccc;
+
+ // Panel
+ --panel-header-background: #ececec;
+ --panel-border-color: #AAA;
+
+ // Process
+ --process-label-background: #7a548d;
+ --process-label-color: #fff;
+
+ --process-label-padding: 0.5rem;
+ --activity-padding: 0.5rem;
+ --gene-product-padding: 0 0 0.5rem 0;
+ --function-label-padding: 0 0 0.5rem 0;
+
+ --graph-padding: 8px;
+
+--panel-header-padding: 8px;
+
+--panel-border-color: #CCC;
+
+--panel-border-width: 1px;
+--process-border-width: 1px;
+
+
+//Legend
+--legend-padding: 8px;
+--legend-header-padding: 8px;
+
+}
+
+
+.gocam-viz-legend-container {
+ padding: 0 1.2rem;
+ width: 800px;
}
\ No newline at end of file