Color legends for VlnPlot and Stacked_VlnPlot

[nikofleischer]

Hi,
I think this is a known issue, but would it be possible to add functionality for labeling the colors when using split.by in VlnPlots or Stacked_VlnPlots?

Best,
Niko

[samuel-marsh]

Hi Niko,

Can you provide example of the issue you are describing?

Best,
Sam

[nikofleischer]

Hey Sam,
sorry I didn't attach one as I saw you were commenting on the same issue over at the Seurat GitHub explaining that their Function doesn't support this. Here you go with the mwe and resulting plots:

library(Seurat)
library(scCustomize)
library(tidyverse)
data("pbmc_small")
pbmc_small %>% VlnPlot_scCustom(features = rownames(pbmc_small)[1:10])
pbmc_small %>% Stacked_VlnPlot(features = rownames(pbmc_small)[1:10])

[samuel-marsh]

Oh sorry do you just want the legend to appear on the plot?

[nikofleischer]

Hey,
sorry I messed the example up and forgot the split.by = 'groups' option.
What I actually meant was:

library(Seurat)
library(scCustomize)
library(tidyverse)
library(patchwork)

data("pbmc_small")
p = list()
p[[1]] = pbmc_small %>% VlnPlot_scCustom(features = rownames(pbmc_small)[1:4],split.by = 'groups') + theme(legend.position = 'bottom')
p[[2]] = pbmc_small %>% VlnPlot_scCustom(features = rownames(pbmc_small)[1:4],split.by = 'groups') & theme(legend.position = 'bottom') 
p[[3]] = pbmc_small %>% Stacked_VlnPlot(features = rownames(pbmc_small)[1:4],split.by = 'groups') + theme(legend.position = 'bottom')
p[[4]] = pbmc_small %>% Stacked_VlnPlot(features = rownames(pbmc_small)[1:4],split.by = 'groups') & theme(legend.position = 'bottom')

wrap_plots(p)

Here we can see that & works to add the legend in both cases, but + only works for VlnPlot and not for Stacked.

Originally I thought it also doesn't work with VlnPlot_scCustom, but this was a problem with patchwork and parentheses as I've just realized. Sorry for that.

[samuel-marsh]

Hi,

So fix for this is now live in the develop branch v0.7.09926. I chose to solve the issue by adding extra parameter to the function. You can now use plot_legend = TRUE in order to display a single legend so stacked vlnplots.

This parameter is still compatible with ggplot/patchwork theming in order to move/edit legend.

If you run into any issues getting this work please let me know and I'll reopen the issue.

Best,
Sam

library(tidyverse)
library(Seurat)
library(scCustomize)

pbmc <- pbmc3k.SeuratData::pbmc3k.final
pbmc <- UpdateSeuratObject(pbmc)

Stacked_VlnPlot(pbmc, c("FOS", "CD3E"), plot_legend = TRUE)

Stacked_VlnPlot(pbmc, c("FOS", "CD3E"), plot_legend = TRUE) & theme(legend.position = "bottom")