How to plot the heat map of a subset of cell types using plotHeatmap from scater package

1

Hi

I'm using plotHeatmap (library(scater)) to visualize the accuracy of cell type annotation output from SingleR. In total I got 28 labels, but as you can see on the top of the plot, the color different is hard to distinguish due to too many labels. I wonder whether there is a simple way to show only 5 to 7 labels in this plot, this is because I only care some specific cell types only, not all of them. For example "AT1 cells, AT2 cells and B cells" are the three cells I'm interested. How to only plot for only three labels?

 Library(scater)  
 plotHeatmap(sce.data.combined.sct, order_columns_by = "labels", features=feature)

heatmap output


scRNAseq


scRNA


SingleR


plotHeatmap


scater

• 76 views



Source link