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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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Use a different colormap/palette in gene expression visualizations #7

Closed wflynny closed 4 years ago

wflynny commented 6 years ago

https://github.com/10XGenomics/cellranger/blob/aba5d379169ff0d4bee60e3d100df35752b90383/lib/python/cellranger/webshim/constants/gex.py#L561

It would be better if instead of Jet, which is a problematic colormap, a perceptually uniform colormap was used. Included in Plotly is Viridis but really any sequential colormap is better than Jet. By choosing a better default, you can hopefully help people move away from using Jet.

evolvedmicrobe commented 4 years ago

We've enabled alternate color schemes in the new Visium product offering, including Viridis (see the analysis tab here: http://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Breast_Cancer_Block_A_Section_1/V1_Breast_Cancer_Block_A_Section_1_web_summary.html). Survey's indicated Jet was still preferred, but we may visit that later.