When it comes to make a heatmap, ComplexHeatmap by Zuguang Gu is my favorite. Check it out! You will be amazed on how flexible it is and the documentation is in top niche.
For Single-cell RNAseq, Seurat provides a DoHeatmap function using ggplot2. There are two limitations:
when your genes are not in the top variable gene list, the
scale.datawill not have that gene andDoHeatmapwill drop those …