Different results with heatmap.2 and pheatmap ?
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
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Can you show us the results of
head(y)andhead(highly_variable_lcpm)?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_lcpmobject before selecting / ordering the subset of genes you want to plot, and then plot asIf you show us your code, we will be able to help more specifically.