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