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MultiQC version 1.21

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@vladsavelyev vladsavelyev released this 28 Feb 13:55
· 79 commits to main since this release
v1.21
abe4d3d

Highlights

Box plot

Added a new plot type: box plot. It's useful to visualise a distribution when you have a set of values for each sample.

from multiqc.plots import box
self.add_section(
    ...,
    plot=box.plot(
        {
            "sample 1": [4506, 4326, 3137, 1563, 1730, 3254, 2259, 3670, 2719, ...],
            "sample 2": [2145, 2011, 3368, 2132, 1673, 1993, 6635, 1635, 4984, ...],
            "sample 3": [1560, 1845, 3247, 1701, 2829, 2775, 3179, 1724, 1828, ...],
        },
        pconfig={
            "title": "Iso-Seq: Insert Length",
        },
    )
)

Note the difference with the violin plot: the box plot visualises the distributions of many values within one sample, whereas the violin plot shows the distribution of one metric across many samples.

pyproject.toml

The setup.py file has been superseded by pyproject.toml for the build configuration.
Note that now for new modules, an entry point should be added to pyproject.toml instead of setup.py, e.g.:

[project.entry-points."multiqc.modules.v1"]
afterqc = "multiqc.modules.afterqc:MultiqcModule"

Heatmap

The heatmap plot now supports passing a dict as input data, and also supports a zlab
parameter to set the label for the z-axis:

from multiqc.plots import heatmap
self.add_section(
    ...,
    plot=heatmap.plot(
        {
            "sample 1": {"sample 2": 0, "sample 3": 1},
            "sample 2": {"sample 1": 0, "sample 3": 0},
            "sample 3": {"sample 1": 1, "sample 2": 0, "sample 3": 1},
        },
        pconfig={
            "title": "Sample comparison",
            "zlab": "Match",
        },
    )
)

MultiQC updates

  • New plot type: box plot (#2358)
  • Add "Export to CSV" button for tables (#2394)
  • Replace setup.py with pyproject.toml (#2353)
  • Heatmap: allow a dict dicts of data (#2386)
  • Heatmap: add zlab config parameter. Show xlab, ylab, zlab in tooltip (#2387)
  • Warn if run_modules contains a non-existent module (#2322)
  • Catch non-hashable values (dicts, lists) passed as a table cell value (#2348)
  • Always create JSON even when MegaQC upload is disabled (#2330)
  • Use generic font family for Plotly (#2368)
  • Use a padded span with nowrap instead of   before suffixes in table cells (#2395)
  • Refactor: fix unescaped regex strings (#2384)

Fixes:

  • Pin the required Plotly version and add a runtime version check (#2325)
  • Bar plot: preserve the sample order (#2339)
  • Bar plot: fix inner gap in group mode (#2321)
  • Violin: filter Inf values (#2380)
  • Table: Fix use of the no_violin (ex-no_beeswarm) table config flag (#2376)
  • Heatmap: prevent from parsing numerical sample names (#2349)
  • Work around call of full_figure_for_development to avoid Kaleido errors (#2359)
  • Auto-generate plot id when pconfig=None (#2337)
  • Fix: infinite dmax or dmin fail JSON dump load in JavaScript (#2354)
  • Fix: dump pconfig for MegaQC (#2344)

New modules

  • IsoSeq
    • Iso-Seq contains the newest tools to identify transcripts in PacBio single-molecule sequencing data (HiFi reads). cluster and refine commands are supported.
  • Space Ranger
    • Works with data from 10X Genomics Visium. Processes sequencing reads and images created using
      the 10x Visium platform to generate count matrices with spatial information.
    • New MultiQC module parses Space Ranger quality reports.

Module updates

  • bcl2fastq: fix the top undetermined barcodes plot (#2340)
  • DRAGEN: add few coverage metrics in general stats (#2341)
  • DRAGEN: fix showing the number of found samples (#2347)
  • DRAGEN: support gvcf_metrics (#2327)
  • fastp: fix detection of JSON files (#2334)
  • HTSeq Count: robust file reading loop, ignore .parquet files (#2364)
  • Illumina InterOp Statistics: do not set 'scale': False as a default (#2350)
  • mosdepth: fix regression in showing general stats (#2346)
  • Picard: Crosscheck Fingerprints updates (#2388)
    • add a heatmap for LOD scores besides a table
    • if too many pairs in table, skip those with Expected status
    • use the warn status for Inconclusive
    • add a separate sample-wise table instead of general stats
    • sort tables by status, not by sample name
    • add a column "Best match" and "Best match LOD" in tables
    • hide the LOD Threshold column
  • PURPLE: support v4.0.1 output without version column (#2366)
  • Samtools: support new coverage command (#2356)
  • UMI-tools: support new extract command (#2296)
  • Whatshap: make robust when a stdout is appended to TSV (#2361)

New Contributors

Full Changelog: v1.20...v1.21

Contributors

grst
Assets 2