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rbioinformaticsviolin-plot

Violin Plot with Genes on the X axis using Defined group of cells

I'd like to ask a question after searching for some time and not finding an answer. This pertains to single-cell RNA sequencing data analysis.

Is it possible to create a violin plot where instead of clusters or cell types on the X axis and normalized expression on the Y axis, one has genes on the X axis, normalized expression on the Y axis, and the cells selected for analysis are user-defined?

For example, say I have 500 cells of celltype "A" which express a generally similar genetic signature but a few genes are variably expressed. Could I visualize gene expression as a violin plot for these 500 cells with genes on the X axis instead of a separated violin plot for each gene, since I'm only looking at one cellular type?

Thanks for any ideas on this one! I looked through scCustomize package as well and didn't find anything that jumped out at me, but it's totally plausible I could have missed something!

Solution

  • I would check out the R programming language, using the program Rstudio, with the Seurat package. They have tons of tutorials that will help people of any coding background. https://satijalab.org/seurat/articles/pbmc3k_tutorial.html There's other great vignettes on that site.