Displaying separate UMAPs for samples processed together

[sylestiel]

Is there a way to generate separate UMAPs for each of the component samples (when looking for a given marker) when multiple scATAC samples are processed together?

Thanks!

[rcorces]

I'm not sure I fully understand. Perhaps you are looking for the highlightCells parameter?

[sylestiel]

This has to do with plotEmbedding function. If I have multiple arrow files combined into a single project but want to see them in separate UMAPs side by side (basically like splitting them to view them simultaneously) is that possible?

[rcorces]

Did you try my suggestion using highlightCells?

plotEmbedding(ArchRProj = projHeme5, embedding = "UMAP", colorBy = "cellColData", name = "Sample")

plotEmbedding(ArchRProj = projHeme5, embedding = "UMAP", colorBy = "cellColData", name = "Sample", highlightCells = getCellNames(ArchRProj = projHeme5)[which(as.character(projHeme5@cellColData$Sample) == "scATAC_BMMC_R1")])

[sylestiel]

I did not know how to use the highlight parameter initially. Thanks for providing this example.