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

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).

Violin Plot

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.

rna-seq seurat violin plot
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updated by ivivek_ngs ivivek_ngs • written by David_emir David_emir

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?

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written by rpolicastro rpolicastro

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

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written by David_emir David_emir

1 answer

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

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written by ivivek_ngs ivivek_ngs

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