Visualise two marker genes on TSNE using Bioconductor
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2.8 years ago
Stavroula • 0

Hello,

I was wondering if there is a way to visualise two marker genes from different clusters in the same tSNE plot using Bioconductor in R?

Bioconductor tSNE • 733 views
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So far I have the code for a single marker gene:

plotTSNE(sce, colour_by = "elav", text_by = "louvain", by_exprs_values = "logcounts")

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There is to my knowledge no in-built function in scater (the package that impements most of these plotting functions) for this. It is also questionable how meaningful such a plot is because a scell (so a dot on the TSNE) can have one color, or another, but how is one dot supposed to have two colors in case the cell expressed two marker genes at high levels? Make it simple, just make two TSNEs and combine them with something like patchwork. Or use alternative plotting routines, see https://bioconductor.org/packages/devel/bioc/vignettes/scater/inst/doc/overview.html#3_Visualizing_expression_values

Sure you could basically stitch some ggplot code together to force one TSNE showing several markers but as said that only makes sense if the expression is very bimodal and one clusters has high expression while all others basically have none.

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