Question: Mapping clonotypes on UMAP
0
gravatar for ecl75
4 months ago by
ecl750
ecl750 wrote:

Hello! I have identified in my seurat object the top 10 clonotypes based on frequency. I used this code to find them

top10_clonotype <- table(Object$clonotype_id)
top10_clonotype <- as.data.frame(top10_clonotype)
top10_clonotype <- slice_max(top10_clonotype, order_by = top10$Freq, n=11)

I would like to then highlight them on my umap. I ran the line-DimPlot(AD007, reduction = "umap", cells.highlight=top10). The number one clonotype frequency came up 22 times yet on the umap there was just one dot for it. Any suggestions? Please and thanks!

rna-seq seurat vdj R • 307 views
ADD COMMENTlink written 4 months ago by ecl750

What does head(top10) and head(top10_clonotype) yield? My guess is that you aren't feeding a vector of cell barcodes to cells.highlight.

ADD REPLYlink modified 4 months ago • written 4 months ago by jared.andrews078.6k
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