We're currently analysing some 10X single cell RNA-seq data using Seurat v3. Using FeaturePlot, I can get UMAP plots for a set of genes comparing Control and Experiment groups, with cells expressing my gene of interest being highlighted and the dot intensity indicating gene expression.
What I'd like to do now however is to generate UMAP plots for both Control and Experiment groups where only those cells are highlighted that coexpress a set of marker genes that I define, so that I show differences in a given cell population in my UMAP plot between both groups. I already found that FeaturePlot can compare two genes and their expression level using the blend attribute - but I don't need any expression level annotation, I just want all cells to be drawn and those who show coexpression (of any level) to be annotated in colour.
What would be the way to do this?
Hi,
Even I am interested in knowing whether I can look at cells that express set of genes. I know there is "filter" option in loupe cell browser, but not sure about Seurat. Did you get to know about it from the time you posted?
Raghu
This would best be posted as a new question so that we can focus on your specific situation.
Not sure how to do it in Seurat. But this kind of work could be done by general data analysis process.