Heatmap for txt data.frame or matrix

Question

[ab123]

Hi guys,

Has anyone managed to generate a heatmap for a txt file (illumina data) read in as a data.frame.

Pheatmap and Heatmap both fail to generate one...

I feel like I'm missing something or doing something wrong.

Any pointers or workarounds would be much appreciated!

Cheers

[venu]

Sure, could you also show your code, otherwise it would be difficult to find out what is going wrong. You could also show some lines from your txt file.

[ab123]

Hey Venu, Thanks for the reply.

I actually managed to make it work with a work-around of this code in case anyone has the same issue.

dists <- as.matrix(dist(t(exp_palmieri), method = "manhattan"))
colnames(dists) <- NULL
diag(dists) <- NA
rownames(dists) <-  pData(palmieri_eset)$Factor.Value.phenotype.
hmcol <- colorRampPalette(rev(brewer.pal(9, "PuOr")))(255)

pheatmap(dists, col = rev(hmcol), clustering_distance_rows = "manhattan",
                    clustering_distance_cols = "manhattan")

[venu]

Glad you figured it out.

Just a note (if you don't think I'm being too hard), you can try several ways on your own to get the solution (Just how you did it now). I know it's tempting to ask for help after failing once or twice but you can definitely find work-arounds with little more effort, at least for the problems like this :)

[WouterDeCoster]

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below: