I have single cell RNA-seq on 8 time points. I have clustered each time point to 2-3 clusters by seurat. I also have a list of differentially expressed genes between all my 1562 cells in 8 time points. I know how to plot this list of genes in heat map on each cluster of cells or a big heat map of my 1562 cells, but I have also sub-clusters for each cluster (time point).
Could you please help me to figure out how can I have a heat map with sub-clusters for each time point on which I am showing a list of differentially expressed genes?
Something like the picture below where each day has been clustered to 2-3 sub-population then they plotted common differentially expressed genes between day points
Lets say 500 genes commonly are being differentially expressed in 8 time point. time point 1 has 3 sub-clusters of cells and time points 2 has 2 sub-clusters of cells. time point 3 and 4 both have 2 sub-clusters of cells. I want to heat map these 500 genes in cells in time point 1 (3 sub-clusters), time point 2 (2 sub-clusters), time point 23 (2 sub-clusters) and time point 4 (2 sub-clusters) in one unified heat map on which cells in each subclusteres (a,b and c) are in column and genes in rows but I don't have any idea how to do that. column annotation function in ComplexHeatmap likely works in this regard But I don't know how to define cells inside each sub cluster in different colours
I can heat map of 500 genes only on time points easily by seurat but without underlying sub clusters
> DoHeatmap(object = SubsetData(object = object, max.cells.per.ident = > 100), genes.use = 50 genes, slim.col.label = TRUE, group.label.rot = > TRUE)
Figure 2 in this article.