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stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data
https://stuartlab.org/signac/
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The normalized signal is zero in CoveragePlot after subset #1711

Closed ZhengJIN94 closed 3 weeks ago

ZhengJIN94 commented 1 month ago

Hi,

I tried to use "subset" function to select several clusters to downstream analysis. However, after "subset", the CoveragePlot seems not correct. What is the correct operation after subset function? I didn't find related tutorial in the website.

Thank you so much if anyone can answer me!

Here is my code to subset

obj_sub <- subset(obj_harmony, idents = c(0, 2, 3, 4, 10, 11, 13, 14))

Here is my code and plot result

Before: CoveragePlot(object = obj_harmony, group.by = 'seurat_clusters', region = "Itgam", window = 20, annotation = TRUE)

image

After: CoveragePlot(object = obj_tumor, group.by = 'seurat_clusters', region = "Gypa", window = 20, annotation = TRUE)

image
timoast commented 1 month ago

Hi @ZhengJIN94, I wasn't able to reproduce this issue. Can you include your full code and output of sessionInfo()?

timoast commented 3 weeks ago

Closing this as I haven't heard back and can't reproduce it, please reopen if you are still having problems and can provide the info requested above