Pathway Expression Analysis on Individual Cells?

Question

[ospinae]

Hello,

I'm very new to sc-RNA-seq analysis on R (and coding in general) and I am trying to analyze a sc-RNA-seq dataset of pancreatic islets (I have been using Seurat v4 for this). My main research question surrounds comparing two pathways in beta cells and seeing if there is a correlation between these pathways. In the end, I hope to have a scatterplot with two pathways and see where each individual cell lands on this plot.

I've made subclusters of my beta cells, but the clustering is not separating out the clusters based on certain levels of pathway expression (which I would prefer because separating those clusters would make everything easier for me to analyze) but I haven't found a way to cluster based on a specific pathway.

So my question is: Is there a way to plot individual cells based on the expression of entire pathways? If not, is there a way to do something similar to accomplish my goals?

Thank you to all that comment--I'm brand new so I would love any advice that I can get.

Answer 1

[jared.andrews07]

You can compute gene set activitites fairly easily. See also the AddModuleScore function from Seurat for a similar function. Then you can just plot the scores for each cell as box/violin/ridgeplots as needed. This will highlight differences between your sub-clusters or groups.

[ospinae]

Thank you so much, Jared! I was able to use AddModuleScore and plot the scatterplot as I needed!