Cannot color cells with 0 expression in certain color

Question

[leranwangcs]

I'm trying to use FeaturePlot() function, but when there is a gene has 0 existence in all cells (the right most one), that plot was colored to a dark scale which I expected it to be all gray.

My command is:

feature.plot <- FeaturePlot(combined.all, features = c("Ifnlr1","Ifnl2","Ifnl3","Stat1","Isg15","Murine-astrovirus-STL1","Murine-astrovirus-STL5"), split.by = "modified.ident", cols = c( "gray","red"),reduction = "tsne")

I saw similar questions and one answer was to modify the cols = c( "gray","red") parameter to cols = c( "gray","gray"), however in that case other plots would not be able to correctly colored.

Is there anyway that I can have the figures combined and also have the correct colors for any scenarios?

Also, I cannot get the legend show up when I use combine = TRUE parameter, is there anyway that I could have a legend show in the combined plot?

Thanks so much! Leran

[Jautis]

There may be some way to change Rs default rounding behavior. My guess would be ggplot generates quantiles corresponding to colors and then applies some variant of "less than/greater than" which is rounded up. There may be some way to adjust that to round down instead, but I'm not aware of it

Answer 1

[shuaizh117]

FeaturePlot(..., keep.scale = "all")