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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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V5 FeaturePlot behaviour #8302

Closed mdeea closed 7 months ago

mdeea commented 7 months ago

I've recently upgraded to Seurat V5. The behaviour of Featureplot wrt colorpalettes seems to have changed. When I supply it with a vector of colours, it just bins the data into two bins corresponding to the maximal and minimal values in the palette. Is there some other option I should be using to get a gradient of colours?

plasma <- viridis(10, direction = 1, option = "C")

FeaturePlot(mySet.combined, reduction = "umap", features = myHallmarks[3], order = TRUE, keep.scale = 'feature', split.by = "Age", cols = plasma ) myUmap.pdf

samuel-marsh commented 7 months ago

Hi,

Not member of dev team but hopefully can be helpful. In terms of applying gradient you can do this as you would with any ggplot2 object with post plot theming.

Alternatively, I have implemented gradient natively in my package scCustomize FeaturePlot_scCustom. It is plasma by default and also shifts non-expressing cells off of the color scale to a different color.

Best, Sam

mdeea commented 7 months ago

Thanks, I had post-hacked it using patchwork but wanted to understand what I was doing wrong.