Cluster columns in Pheatmap
1
0
Entering edit mode
pehove2385 • 0
@8428faaa
Last seen 2 days ago
Switzerland

Hi all. I'm new to this kind of analysis so maybe will be silly.

I'm trying to group the columns of my Pheatmap. My dataframe contains expression level of genes in different condition: timepoint (24h,48h,72h) and treatment (untreated and treated). My Pheatmap has 6 columns in this way: treated.24h, treated.48h, treated.72h, untreated24h, untreated48h, untreated 72h. Instead, I only want two columns: treated and untreated (grouping all timepoints).

For example, I can do this very easily with boxplot:


boxplot(unlist(mydataframewithgenes["GENE",] ~ treatment))

is there a similar way to obtain this with pheatmap? Something like

pheatmap(mydataframewithgenes ~ treatment)

Which sadly doesn't work.

Thanks in advance!

geneexp pheatmap heatmaps cluster • 200 views
ADD COMMENT
0
Entering edit mode

Hi,

You mean to take the average expression of each group per gene and plot only 2 columns with averages?

ADD REPLY
0
Entering edit mode
@james-w-macdonald-5106
Last seen 14 hours ago
United States

This support site is meant for helping people with Bioconductor packages, and pheatmap isn't one of them, so you should be posting on biostars.org rather than here.

Login before adding your answer.

Traffic: 864 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6