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s-andrews / FastQC

A quality control analysis tool for high throughput sequencing data
GNU General Public License v3.0
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Add colourblind friendly palletes, activated with --colourblind #91

Closed jamesabbott closed 2 years ago

jamesabbott commented 2 years ago

Hi Simon,

We use fastqc as part of both our UG and PG teaching, and I'm trying to improve accessibilty to the tools we use, and the combination of red and green in some of the fastqc plot is a bit problematic.

This PR makes uses of a colourblind-friendly colour schemes (from https://personal.sron.nl/~pault/#sec:qualitative) when generating linegraph or qualitybox plots. Colourblind palettes tend to be a bit garish to the unaffected eye, so I've tried to select colours that don't look too horrific, and the default behaviour is unchanged. The cb-friendly palettes are only used when the --colourblind argument is provided on the command line.

I've not done anything to the tile plots since the cb-friendly palettes are more limited in available colours, and I don't think there is such a problem there compared to the red/green combinations in the line plots.

Hopefully you will be happy to include these changes in the main fastqc codebase.

s-andrews commented 2 years ago

In 05c253d I've changed the colours used to be colourblind friendly by default rather than adding a new command line option. The colours were taken from https://davidmathlogic.com/colorblind/