Visualize overall distribution of all genes

[royfrancis]

I would like to plot the overall distribution of all genes. For example, VlnPlot() for all genes. I know how to do this manually, but is there a plotting function for this, that I might have missed?

[timoast]

I'm not sure what you mean, can you clarify or give an example?

[royfrancis]

A violin plot showing expression distribution for all genes.

library(Seurat)
library(ggplot2)
x <- data.frame(value=as.vector(as.matrix(GetAssayData(pbmc_small,slot="data"))))
x$sample <- "sample"
ggplot(x,aes(x=sample,y=value))+
  geom_violin()

So, I was expecting something like this with the Seurat violin plot function

Seurat::VlnPlot(pbmc_small)
Error in ExIPlot(object = object, type = ifelse(test = split.plot, yes = "splitViolin",  : 
  argument "features" is missing, with no default

without any features specified to display all features.

[timoast]

We don't have a function to do that. Since it involves converting the sparse matrix to a dense representation, this could require huge amounts or memory for larger datasets, so I don't think we will add this as a function in Seurat, especially since it can be done easily as you've shown