Seurat: DotPlot only show gradient of grey, when the value in split variable contains '_'

[shendong124]

Hi Seurat Team,
I am trying to use Dot plot on my dataset and it seems that I can not get any other vcolors than gradient of greys.
here is my code:

DotPlot(mergetest2.big, features = rev(markers.to.plot), cols = c("blue", "red", "blue"), dot.scale = 8,
split.by = "orig.ident") + RotatedAxis()

and the result:

Thank you very much
Shen

[MediciPrime]

I have the same question. I am trying to create a DotPlot using data from an integrated Seurat analysis but for some reason I can only see a single grey color gradient. Here is my code used to create my dotplot:
DotPlot(combined, features=genes, dot.scale = 8, split.by = 'stim', cols = c('blue', 'red', 'green', 'navy', 'orange', 'purple')) + RotatedAxis()

Please help

[osvobod]

Hi,
I have the same problem. Have you been able to find any solution to this?
Thank you,

Ondrej

[shendong124]

Hi Satijalab/Seurat team,

I am still having this issue....

Shen

Le ven. 14 juin 2019 à 09:47, osvobod [e-mail] a écrit :

Hi,
I have the same problem. Have you been able to find any solution to this?
Thank you,

Ondrej

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[shendong124]

Never mind. It is working now.
I actually have not changed anything that I am sure made a difference. I just specified the genes for features. Also maybe library(ggplot2)?

here is my code:
DotPlot(merge007001.big, features = c("CD247", "CD3E", "CD3D", "CD3G", "CD8B", "CD8A", "CD79A", "CD79B", "HLA-DRA", "CD27", "CD28", "CD4"), cols = c("blue", "red", "green"), split.by = "orig.ident")

Hope it will work for you :)
Shen

[Liuy12]

I encountered similar issues. Turns out that if you have '_' in your split variable, the color scheme will not work. This seems to be a bug.

[shendong124]

Yes indeed!!
Thank you for the clarification!!!

Shen

[danmoore1987]

Dear Seurat team, it appears that this bug has not been resolved, even the latest Seurat (3.1.2) yields the same problem.

[owenwilkins]

this is a most annoying bug

[yuhanH]

Thanks for @Liuy12 's answer. If the value in your split variable contains '_', the color scheme will not work. We will fix this bug soon.

[satijalab]

Closing as this is a duplicate