How to use DoHeatmap function for cell type clustering(clustering columns based on identity)?

[Rui-Jing]

Hi,
Thanks for developing this great single cell tools. I have three questions about DoHeatmap fuction.

1. How do I cluster the columns(by cell identity) when I select some genes to run DoHeatmap? Specifically, I would like to see more similar expression cell ientities clustered together under the premise of customized genes.

2. When I use the DoHeatmap function to cluster my single-cell data(350genes, 39588cells), there is no graphic display.

3.How can I change the color scheme of the entire heatmap(Not yellow and purple)?

Thanks!

[samuel-marsh]

Hi,

Not member of dev team but hopefully can be helpful.

1. This isn't currently supported with the Seurat function. If you are interested in performing this or other more advanced heatmap functionality I would encourage you checking out other heatmap packages (pheatmap, ComplexHeatmap, etc)

2. I would anticipate this is simply slow plotting due to the number of cells included in the plot meaning it's very large. You could try saving the plot directly into file and then opening file vs. waiting for it to render in RStudio.

3. You can change the color scheme like other ggplot2 based objects. See Adjusting DoHeatMap color scale #1531

Best,
Sam

[torkencz]

Hi,
I would also recommend ComplexHeatmap for your first point. For a large number of cells I recommend sampling down if you want to see the graphical output. Otherwise I recommend saving to a file. Use ggplot color scale to modify heatmap colors.