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Question: Sub clustering from hierarchical cluster used to make heat map of gene expression data
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gravatar for lawarde.ankita1
9 months ago by
lawarde.ankita120 wrote:

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?

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