Heatmap of Top Genes

[helpmeplsxoxo]

I have been using the plotMarkerHeatmap function to plot the heatmap for my ATAC data, but it is very hard to interpret with so many genes. How can I only make a heatmap with the top 10 genes per cluster?

Thanks!

[rcorces]

I'm not sure this is what you are looking for but the nPrint parameter sounds close:

nPrint	If provided seMarker is from "GeneScoreMatrix" print the top n genes for each group based on how uniquely up-regulated the gene is.

If thats not what you mean, you will likely need to plot the heatmap manually.

[rcorces]

or trim your seMarker to only have the genes you want to plot

[helpmeplsxoxo]

Yes, I think I need to trim my seMarker. Is there a specific argument in the GetMarkerFeatures function to use to trim it?

[rcorces]

No you would trim it manually using standard SummarizedExperiment manipulations.