Different results with heatmap.2 and pheatmap ?

Question

[Björn]

I got two completely different results (gene numbers) using heatmap.2 and pheatmap commands while doing DE analysis in edgeR

heatmap.2 command:

heatmap.2(highly_variable_lcpm,labRow = rownames(y$genes),Rowv = TRUE,  col=rev(morecols(20)),trace="column",tracecol = "black",main="Top 20 most variable genes across samples",ColSideColors=group.col,scale="row",margins=c(10,5))

Graph:![heatmap_graph][1] [1]: https://ibb.co/h8BqoH

pheatmap command:

pheatmap(highly_variable_lcpm,labRow = rownames(y$genes),Rowv = TRUE,  col=rev(morecols(20)),trace="column",tracecol = "black",main="Top 20 most variable genes across samples",ColSideColors=group.col,scale="row",margins=c(10,5), cutree_rows = 4)

Graph![enter image description here][1] [1]: https://ibb.co/gTgjFx

Additionally, How to convert the row-names to real gene names. The "labRow" don't seem to work ! Thanks Björn

[Carlo Yague]

Can you show us the results of head(y) and head(highly_variable_lcpm) ?

[h.mon]

The problem probably stems from the fact that you are using two different objects for the measurements and gene names. You should transfer gene names (as row names) to the highly_variable_lcpm object before selecting / ordering the subset of genes you want to plot, and then plot as

heatmap.2( highly_variable_lcpm, labRow = rownames(highly_variable_lcpm), ...

If you show us your code, we will be able to help more specifically.