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biocore / empress

A fast and scalable phylogenetic tree viewer for microbiome data analysis
BSD 3-Clause "New" or "Revised" License
45 stars 31 forks source link

Support discretization as an alternative to continuous coloring #556

Open fedarko opened 2 years ago

fedarko commented 2 years ago

Just to track this as a separate feature, independent of #521.

From @mortonjt in https://github.com/biocore/empress/issues/521#issuecomment-1128942024:

But I do want to note that discretizing colors in heatmaps is actually the recommended practice for visualization. If you look at any COVID heatmap, all of the reported journals have discretized colors

This one is from NPR

image

And this one is from Mayo clinic image

So when thinking through these use cases, I wouldn't recommend completely throwing out the idea of discretizing continuously value quantities.

From @kwcantrell:

Thats a good idea! We can create a UI to easily enable discretizing continuously valued quantities. I think it would also be nice to upload a json that can set different parameters.

From @antgonza:

If we are rethinking coloring (which might also help in Emperor); AFAIK both tools share background design ... what about allowing (via the GUI) to split the values in quartiles or deciles?

From @kwcantrell:

Thats kinda what I was thinking. We can add a 'buckets' option were users can define how many discrete regions they want and also define the bounds of the regions.