I am using Rstudio to create heatmap for some expression data; My file includes 38 genes, therefore, 38 rows and 20 columns as samples. The output heatmap shows only 19 of my genes!!!
Any idea how this might happen?
my R codes:
x row.names(x) x y hr hc heatmap(y, Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc), col=myheatcol, ColSideColors=heat.colors(length(hc$labels)), scale="col")
I don't have this issue when running Pheatmap on the same data!
Something is wrong with my code?
I will appreciate your suggestions,
Mah
Hi Mahbobeh zamani babgohari . There are some missing parts in your code. Where did sc_y come from?
My best guess is that you missing some genes when you create sc_y.
For example if you run the code above you will see a heatmap with exactly 38 rows and 20 columns.
test
I don't have access to your dataset but judging by the third line of your code, you're only selecting rows 1:20.
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