Sub clustering from hierarchical cluster used to make heat map of gene expression data
0
0
Entering edit mode
@lawardeankita1-14844
Last seen 16 months ago
Estonia

Hello Sir/madam,

I'm using R to plot a heatmap of Differentially expressed genes of microarray data and RNA seq data.

i have used heatmap.2 of gplots to plot the heatmap.

My question is,

1. now i want to extract the subcluster from the gene and sample clusters. Uisng this link https://www.biostars.org/p/86563/ i have obtained the clusters using cutree option. but i want to extract those clusters and then plot them again using heatmap.2.

2. i want to extract that subcluster matrix, so how to do that?

Any help with this subcluster extraction would be helpful in terms of R code.

I have used this one R code from the heatmap.2 help to produce the subcluster,

## plot a sub-cluster using the same color coding as for the full heatmap

full <- heatmap.2(x) heatmap.2(x, Colv=full$colDendrogram[[2]], breaks=full$breaks) # column subset heatmap.2(x, Rowv=full$rowDendrogram[[1]], breaks=full$breaks) # row subset heatmap.2(x, Colv=full$colDendrogram[[2]], Rowv=full$rowDendrogram[[1]], breaks=full$breaks) # both

but when i plot this obtained subcluster using heatmap.2 function, the pattern i observed for this subcluster earlier in the master heatmap is not same in the heatmap of subcluster.

3. so if i extract the subcluster and after plotting will the pattern i observed in the master heatmap change?

heatmap.2 hierarchical clustering microarray RNA seq DEG • 1.8k views
ADD COMMENT

Login before adding your answer.

Traffic: 1093 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