Surat object UMAP - highlight cells based on Citeseq data

Question

[chi.delta]

Hello,

I am trying to visualize a specific cell subset on my UMAP depending on the a cite seq antibody staining and usually I do that using the FeaturePlot() function. However I dont want to show the expression in a color scale but would rather visualize all the cells that show any level of expression of the surface marker with a single color.

Is this possible? I tried the WhichCells function in order to subset all the cells that express the cite seq marker but the expression argument can ony recognize features from the RNA assay.

Thanks a lot

[antonioggsousa]

Hi,

I never worked with CITE-seq data, but if I understood it you've scRNA-seq data and for the same cells you also have epitopes/proteins, right?

Did you integrate this multimodal data set into one data set in Seurat? If so, you should be able to get the cells expressing or with the markers that you're interested in based on some Seurat function. If not, if you have this data imported into R it is just a question of querying a dataframe/matrix as you normally do in R in order to get the cells that hold the epitope/marker that you want.

Once that you've the cell barcodes/ids that express/hold your marker(s) of interest, you can plot and highlight this in a UMAP by doing:

DimPlot(object = seu, reduction = "umap", label = TRUE, cells.highlight = list("marker" = cells_2_highlight), cols.highlight = "darkred", cols= "grey")

Where seu is your Seurat object with a UMAP and cells_2_highlight is a character vector with the cell barcodes/ids expressing/holding the marker of interest.

I hope this helps,

António