My question is very simple. When I use the clustering option in pheatmap, for example:
res<-pheatmap(matrix, scale="row", cluster_cols=FALSE, show_rownames=FALSE, cutree_rows=8, color=colorRampPalette(c("red","black","green"))(50), cellwidth=30, cellheight=0.4, main="C2C7_Differential_Gene_Expression", fontsize=4,filename="C2C7_Differential_Gene_Expression8clusters.pdf")
I get a cool heatmap image with 8 differentiated clustes. These clusters however are not labeled. After writing the data to a file:
b<-data.frame(cutree(res$tree_row, k=8)) write.table(as.data.frame(b), file="C2C7_Differential_Gene_Expression8clusters.txt", sep="\t")
I assumed cluster 1 in this file should be the top cluster in the image. This turns out to not be the case. I think the cluster numbers in the file are ordered based on the tree branching.
As I do not want to waste time figuring out which cluster number corresponds to which cluster in the image, I wonder: Is there an option in pheatmap to label the clusters in the image?