Seurat :Violin plot showing relative expression of select differentially expressed genes

Question

[David_emir]

Hi All, I am working on Single-cell data and I am using Seurat for the data analysis. I want a Violin plot showing relative expression of select differentially expressed genes (columns) for each cluster as shown in the figure (rows) (all Padj < 0.05).

It would be really helpful if you can let me know how to plot as shown in the image.

Thanks a lot for your kind help,

Dave.

[rpolicastro]

By differentially expressed genes, do you mean genes that are unique to a cluster, or genes within a cluster that vary between two or more conditions?

[David_emir]

Thanks a lot for your kind reply, Differential Genes within a cluster that vary between Clusters.

Answer 1

[ivivek_ngs]

Hi,

The above plot isn’t from Seurat AFAIK, it is from scanpy(). Last time I checked this multi gene plot function wasn’t available but one can play around and generate it. Ming has a blog post with code around ggplot(). If you are not familiar with python and underlying packages of single cell there then with Rstats and Seurat() along with other packages you can still produce it. Please check the below link to have the code snippet and try it out at your end. Good luck.

Multi gene violin plot