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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

Threshold feature metadata coloring #209

Open sjanssen2 opened 4 years ago

sjanssen2 commented 4 years ago

I very much like the ability to color sub-trees according to their uniqueness regarding metadata categories. I think it would be even more useful if I could somewhere define a minimal number of reads (or better: percentage of relative abundance) that the combined features in that subtree should have to be colored. Thus, I could ignore features with only a handful of reads and focus on those that might have a biological impact.

antgonza commented 4 years ago

Agreed! In fact, I was thinking that it would be really cool if it would be possible to actually color or change line width based on relative abundance. The specific use case I had in mind: a longitudinal dataset that changes the abundance of a specific group over time; this could be super cool in an animation! Tentative dataset: diet or probiotics.

ElDeveloper commented 4 years ago

This makes sense, would be together with tree collapsing features, right?

antgonza commented 4 years ago

IMOO, I guess it will depend on the user, right? In some cases, the user would like to see it all genera (collapsed) and sometimes all species/strands (tips) ...

ElDeveloper commented 4 years ago

Gotcha, so this is in general a threshold of how many tips constitute a clade's color based on feature metadata.