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Add mosdepth heatmap to MultiQC report #196

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drpatelh opened this issue May 14, 2021 · 2 comments
Closed

Add mosdepth heatmap to MultiQC report #196

drpatelh opened this issue May 14, 2021 · 2 comments
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enhancement Improvement for existing functionality

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@drpatelh
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Would be awesome if we can include the mosdepth amplicon coverage heatmap in the MultiQC report too. Just need to export the matrix from the custom R script we are using by adding a line or two. Can then create custom content for MultiQC to chomp like we are doing in the rnaseq pipeline for the DESeq2 heatmap.

@ewels pointed to some colour codes to get the same palette as in the PDF heatmap:
"Here are the colour codes for the blue-yellow (viridis) colour scale:
https://jarrettmeyer.com/2018/08/07/viridis-color-palette

Get a list of 12 or so of them and set them as the colour_stops config option (or something like that it was, maybe check the docs)"

@drpatelh drpatelh added the enhancement Improvement for existing functionality label May 14, 2021
@ewels
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ewels commented May 14, 2021

https://multiqc.info/docs/#heatmaps - colstops 👍🏻

@drpatelh
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Added in #202

Nanopore test data:

Original PDF

image

In MultiQC

image

Illumina data

The scales look a little different but it's something I can live with

Original PDF

image

In MultiQC:

image

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