pheatmap needs to be manually added to plot heatmaps

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muad.abdelhay ▴ 10

@muadabdelhay-14075

Last seen 4.5 years ago

On SingleR_1.0.5 running plotScoreHeatmap(pred.sce) outputs following error and plots a corrupt heatmap:

Error in UseMethod("depth") : 
  no applicable method for 'depth' applied to an object of class "NULL"

running library(pheatmap) (pheatmap_1.0.12) resolves the issue

singler bug • 1.4k views

ADD COMMENT • link 4.6 years ago muad.abdelhay ▴ 10

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Sorry for the delay.

In v1.0.5 (and pretty nearly still), pheatmap::pheatmap() was called only at the very end of the function. So this issue sounds ultimately like a pheatmap bug.

Anyway, SingleR is a few versions later now, but I can try to help find the root of this bug if you can give me more details.

First, do you still get the bug in SingleR_1.2.0? Second, can you provide a reproducible example along with your sessionInfo()?

ADD REPLY • link 4.6 years ago dbunis ▴ 10

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