Human and mouse on one circle
Two genomes on one circle, their liftOver chain as ribbons.
View source — 58 lines
import {
JBrowseCircularGenomeView,
useCreateViewState,
} from '@jbrowse/react-circular-genome-view2'
const tracks = [
{
type: 'SyntenyTrack',
trackId: 'hg38ToMm39_liftover',
name: 'hg38 to mm39 liftOver chain',
assemblyNames: ['mm39', 'hg38'],
adapter: {
type: 'PairwiseIndexedPAFAdapter',
uri: 'https://jbrowse.org/ucsc/hg38/liftOver/hg38ToMm39.over.pif.gz',
csi: true,
queryAssembly: 'mm39',
targetAssembly: 'hg38',
},
},
]
const chromosomes = [
'chr1',
'chr2',
'chr3',
'chr4',
'chr5',
'chr6',
'chr7',
'chr8',
'chr9',
'chr10',
'chr11',
'chr12',
'chr13',
'chr14',
'chr15',
'chr16',
'chr17',
'chr18',
'chr19',
'chrX',
]
export default function CircularSynteny() {
const state = useCreateViewState({
jbrowseHub: ['hg38', 'mm39'],
tracks,
view: {
height: 700,
displayedRegionNames: chromosomes,
minAlignmentLength: 100_000,
tracks: ['hg38ToMm39_liftover'],
},
})
return state ? <JBrowseCircularGenomeView viewState={state} /> : null
}