Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Improved read cloud display for long reads with inversions (#3707)
- Loading branch information
Showing
26 changed files
with
913 additions
and
922 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
85 changes: 85 additions & 0 deletions
85
plugins/alignments/src/LinearReadCloudDisplay/drawLongReadChains.ts
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,85 @@ | ||
| import { getConf } from '@jbrowse/core/configuration' | ||
| import { max, min } from '@jbrowse/core/util' | ||
| import { Assembly } from '@jbrowse/core/assemblyManager/assembly' | ||
| import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view' | ||
|
|
||
| // locals | ||
| import { ChainData } from '../shared/fetchChains' | ||
| import { LinearReadCloudDisplayModel } from './model' | ||
| import { fillColor, strokeColor } from '../shared/color' | ||
| import { fillRectCtx, strokeRectCtx } from './util' | ||
|
|
||
| export function drawLongReadChains({ | ||
| ctx, | ||
| self, | ||
| chainData, | ||
| view, | ||
| asm, | ||
| }: { | ||
| ctx: CanvasRenderingContext2D | ||
| self: LinearReadCloudDisplayModel | ||
| chainData: ChainData | ||
| view: LinearGenomeViewModel | ||
| asm: Assembly | ||
| }) { | ||
| const distances: number[] = [] | ||
| const minXs: number[] = [] | ||
| const { chains } = chainData | ||
| const { height } = self | ||
| const featureHeight = getConf(self, 'featureHeight') | ||
|
|
||
| // get bounds on the 'distances' (pixel span that a particular split long | ||
| // read 'chain' would have in view) | ||
| for (const chain of chains) { | ||
| let minX = Number.MAX_VALUE | ||
| let maxX = Number.MIN_VALUE | ||
| for (const elt of chain) { | ||
| const refName = asm.getCanonicalRefName(elt.refName) || elt.refName | ||
| const rs = view.bpToPx({ refName, coord: elt.start })?.offsetPx | ||
| const re = view.bpToPx({ refName, coord: elt.end })?.offsetPx | ||
| if (rs !== undefined && re !== undefined) { | ||
| minX = Math.min(minX, rs) | ||
| maxX = Math.max(maxX, re) | ||
| } | ||
| } | ||
| const distance = Math.abs(maxX - minX) | ||
| distances.push(distance) | ||
| minXs.push(minX) | ||
| } | ||
|
|
||
| const maxD = Math.log(max(distances)) | ||
| const minD = Math.max(Math.log(min(distances)) - 1, 0) | ||
| const scaler = (height - 20) / (maxD - minD) | ||
| const halfHeight = featureHeight / 2 - 0.5 | ||
|
|
||
| // draw split long read 'chains' as connected entities | ||
| for (let i = 0; i < chains.length; i++) { | ||
| const chain = chains[i] | ||
| const w = distances[i] | ||
| const top = (Math.log(w) - minD) * scaler | ||
| const min = minXs[i] | ||
| fillRectCtx(min - view.offsetPx, top + halfHeight, w, 1, ctx, 'black') | ||
| const c1 = chain[0] | ||
| let primaryStrand: undefined | number | ||
| if (!(c1.flags & 2048)) { | ||
| primaryStrand = c1.strand | ||
| } else { | ||
| const res = c1.SA?.split(';')[0].split(',')[2] | ||
| primaryStrand = res === '-' ? -1 : 1 | ||
| } | ||
| for (const v0 of chain) { | ||
| const ra = asm.getCanonicalRefName(v0.refName) || v0.refName | ||
| const rs = view.bpToPx({ refName: ra, coord: v0.start })?.offsetPx | ||
| const re = view.bpToPx({ refName: ra, coord: v0.end })?.offsetPx | ||
| if (rs !== undefined && re !== undefined) { | ||
| const w = Math.max(re - rs, 2) | ||
| const l = rs - view.offsetPx | ||
| const effectiveStrand = v0.strand * primaryStrand | ||
| const c = | ||
| effectiveStrand === -1 ? 'color_rev_strand' : 'color_fwd_strand' | ||
| strokeRectCtx(l, top, w, featureHeight, ctx, strokeColor[c]) | ||
| fillRectCtx(l, top, w, featureHeight, ctx, fillColor[c]) | ||
| } | ||
| } | ||
| } | ||
| } |
Oops, something went wrong.