Press n or j to go to the next uncovered block, b, p or k for the previous block.
| 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 | 4x 4x 4x 1x 1x 1x 15x 15x 15x 2x 2x 2x 1x 1x 4x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 2x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 2x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 2x 1x 1x 1x 1x 1x 1x 2x 2x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x | /**
* The map report's MultiQC sections: custom-content files a pipeline's
* MultiQC picks up by their `_mqc` suffix and lays out per sample.
*
* Four files, each from the run's own outputs and nothing else, so a batch of
* `chromosomix mapreport` over a hundred libraries is one MultiQC report with
* a row each: the general statistics (`summary_mqc.tsv`), the resolution ladder
* as a table (`resolutions_mqc.tsv`), the count 80 % of bins reach against the
* bin size (`resolution_mqc.json`) and P(s) (`ps_mqc.json`). Their ids start
* `chromosomix_`, so MultiQC files every sample's under one section.
*
* Numbers, as the report is: no column carries a colour scale that would read
* as a pass or a fail.
*/
import type { CurveOutput, TableOutput, TaskResult } from '../types'
function table(result: TaskResult, id: string): TableOutput | undefined {
return result.outputs.find((output): output is TableOutput => output.kind === 'table' && output.id === id)
}
function curve(result: TaskResult, id: string): CurveOutput | undefined {
return result.outputs.find((output): output is CurveOutput => output.kind === 'curve' && output.id === id)
}
/** A cell of a TSV: a number as it is, a word without the characters TSV cannot hold. */
function cell(value: string | number | undefined): string {
if (value === undefined) return ''
if (typeof value === 'number') return Number.isFinite(value) ? String(value) : ''
return value.replace(/[\t\r\n]+/g, ' ')
}
/** The general statistics: one row for this library, the measures MultiQC's top table shows. */
export function multiqcSummary(result: TaskResult, sample: string): string {
const rows = table(result, 'report-summary')?.rows ?? []
const map = (measure: string): Record<string, string | number> | undefined =>
rows.find((row) => row.group === 'Map' && row.measure === measure)
const ladder = table(result, 'report-resolutions')?.rows ?? []
const finest = ladder.length > 0 ? ladder[ladder.length - 1] : undefined
const columns: Array<[string, string, number | undefined]> = [
['contacts', 'Contacts', map('contacts')?.value as number | undefined],
['cis_share', 'Cis share', map('cis')?.share as number | undefined],
['trans_share', 'Trans share', map('trans')?.share as number | undefined],
['cis_10kb_share', 'Cis ≥ 10 kb share', map('cis, bins ≥ 10 kb apart')?.share as number | undefined],
['finest_bp', 'Finest bin (bp)', finest?.binsize as number | undefined],
['finest_median', 'Median contacts per finest bin', finest?.median as number | undefined],
['finest_reached80', 'Contacts 80 % of finest bins reach', finest?.reached80 as number | undefined],
]
const header = [
"# id: 'chromosomix_mapreport_summary'",
"# section_name: 'chromosomix map report'",
"# description: 'The library, counted from the contact map by chromosomix mapreport.'",
"# plot_type: 'generalstats'",
'# pconfig:',
...columns.flatMap(([key, title]) => [`# - ${key}:`, `# title: '${title}'`]),
]
return [
...header,
['Sample', ...columns.map(([key]) => key)].join('\t'),
[cell(sample), ...columns.map(([, , value]) => cell(value))].join('\t'),
'',
].join('\n')
}
/** The resolution ladder, a row per bin size, named by the sample and the size. */
export function multiqcLadder(result: TaskResult, sample: string): string {
const ladder = table(result, 'report-resolutions')
const columns = ladder?.columns.filter((column) => column.key !== 'binsize') ?? []
return [
"# id: 'chromosomix_mapreport_resolutions'",
"# section_name: 'Resolutions, coarsest to finest'",
"# description: 'Contact ends per bin at each bin size: a contact counts once at each of its two bins. No threshold is applied.'",
"# plot_type: 'table'",
['Sample', ...columns.map((column) => column.label)].join('\t'),
...(ladder?.rows ?? []).map((row) =>
[cell(`${sample} · ${row.binsize} bp`), ...columns.map((column) => cell(row[column.key]))].join('\t'),
),
'',
].join('\n')
}
/** The count 80 % of bins reach, against the bin size: one line per library. */
export function multiqcResolution(result: TaskResult, sample: string): string {
const rows = table(result, 'report-resolutions')?.rows ?? []
const data: Record<string, number> = {}
for (const row of [...rows].sort((a, b) => Number(a.binsize) - Number(b.binsize))) {
const value = Number(row.reached80)
if (value > 0) data[String(row.binsize)] = value
}
return `${JSON.stringify(
{
id: 'chromosomix_mapreport_resolution',
section_name: 'Contacts per bin, by bin size',
description:
'The largest count at least 80 % of bins hold, at each bin size (Rao et al. 2014’s criterion, as a number).',
plot_type: 'linegraph',
pconfig: {
id: 'chromosomix_mapreport_resolution_plot',
title: 'chromosomix: contacts reached by 80 % of bins',
xlab: 'Bin size (bp)',
ylab: 'Contacts per bin',
xlog: true,
ylog: true,
},
data: { [sample]: data },
},
null,
1,
)}\n`
}
/** P(s), as the P(s) task computed it: one line per library, or per sequence where it drew several. */
export function multiqcPs(result: TaskResult, sample: string): string {
const ps = curve(result, 'report-ps')
const data: Record<string, Record<string, number>> = {}
for (const series of ps?.series ?? []) {
const name = (ps?.series.length ?? 0) > 1 ? `${sample} · ${series.name}` : sample
const points: Record<string, number> = {}
for (let k = 0; k < series.x.length; k++) {
if (Number.isFinite(series.y[k]) && series.y[k] > 0) points[String(series.x[k])] = series.y[k]
}
data[name] = points
}
return `${JSON.stringify(
{
id: 'chromosomix_mapreport_ps',
section_name: 'Contact probability P(s)',
description: 'As the chromosomix P(s) task computes it over the whole genome.',
plot_type: 'linegraph',
pconfig: {
id: 'chromosomix_mapreport_ps_plot',
title: 'chromosomix: P(s)',
xlab: ps?.xLabel ?? 'Genomic separation (bp)',
ylab: ps?.yLabel ?? 'P(s)',
xlog: true,
ylog: true,
},
data,
},
null,
1,
)}\n`
}
|