do_DotPlot Sequential palette, diverging, white on extreme low end

[ShashTrip1]

I am running the following code:

do_DotPlot(alldata,features = c("P2RY12","CX3CR1","TMEM119","CSF1R","CD3E","TNF","TNFSF10","IFNG","GZMA","PRF1","FASLG","NKG7","CD163","TGFB1","IL10","HAVCR2","TIGIT","LAG3","PDCD1","CD274","LAIR1","STAT3","ITGAX","HLA-DRA","B2M","TAPBP","HSPA5","CALR","CIITA","CD14","MRC1","FCGR3A","FCGR1A","ITGAV"),sequential.palette = "RdGy",dot_border = TRUE,scale = TRUE,scale.by = "size")+ theme(axis.text.x = element_text(angle = 90,face = "plain",hjust=1,vjust = 0.5),axis.text.y = element_text(face = "plain"),panel.border = element_rect(colour = "black", fill=NA, size=1),legend.text = element_text(face = "plain"))

and the -2 value is showing as white instead of dark red, this is occur with all the diverging color palettes.

[enblacar]

Hi @ShashTrip1,

Thanks for using my package!

I see where the problems is:

• You are feeding a diverging palette to sequential.palette parameter. Normally, this should throw an error, but somehow it is not happening. I will fix that for the next update.
• Since the error is not being called, you actually get the side effect of the diverging palette being treated as sequential, for which I add a white and black end to the palette. That is why you are getting the error.

I did not intend this function to accept diverging palettes, as I thought there was no use case for it. I will implement its usage for the next update. For now, I would suggest you to use a sequential palette.

However, if you really want to use it with a diverging palette, given the side effect, you can just remove the behaviour of adding the white and black end to sequential color palettes with:

options("SCpubr.ColorPaletteEnds" = FALSE)

This should give you the output you want. But please, be mindful that when I update to fix this side effect, this will no longer work. Here is an example:

Current behaviour

options("SCpubr.ColorPaletteEnds" = TRUE)
SCpubr::do_DotPlot(sample, features = Seurat::VariableFeatures(sample)[1:10], sequential.palette = "RdBu")

Hotfix

options("SCpubr.ColorPaletteEnds" = FALSE)
SCpubr::do_DotPlot(sample, features = Seurat::VariableFeatures(sample)[1:10], sequential.palette = "RdBu")

Hope that works! Feel free to reopen the issue if not!

Best,
Enrique