Question: I would like to download list of Heatmap.
0
gravatar for junghyunshim
13 days ago by
junghyunshim0 wrote:

Hi, I have made successfully a heatmap of gene expression comprising of about 600 genes. The 600 genes were clustered and the order is changed from input data list. In the heatmap, I can't see the order because the 600 gene names are overlapped. Now I would like to see or download the new list of the genes in excel or text. Kindly let me know how to do it. Thanks!^^

snp rna-seq R gene • 126 views
ADD COMMENTlink modified 13 days ago • written 13 days ago by junghyunshim0

Which heatmap function did you use? This is important. For example, here is how to do it with pheatmap: A: extract dendrogram cluster from pheatmap

ADD REPLYlink written 13 days ago by Kevin Blighe39k

Thanks for your reply. I used the script as below.

heat2<-heatmap.2(as.matrix(Shoot2), density.info="none", scale="row", trace="none", dendrogram="row", Rowv=T, Colv=FALSE,cexRow=1, col=myPalette, margins=c(11,24))

And I followed the script which you attached, I don't get anything.

    rownames(Shoot2[heat2$tree_row[["order"]],])

character(0)
ADD REPLYlink modified 12 days ago by genomax64k • written 12 days ago by junghyunshim0

I used the heatmap.2 as below.

heat2<-heatmap.2(as.matrix(Shoot2), density.info="none", scale="row", trace="none", dendrogram="row", Rowv=T, Colv=FALSE,cexRow=1, col=myPalette, margins=c(11,24))

I got it using below.

colnames(dat)[out$colInd]

I can get the list only. How can I get all the matrix according to the list? I copied and pasted the list to excel and get the matrix data from the original file using v-lookup. It took a while for re-arranging the list from R to one column of excel. Thanks!!!

ADD REPLYlink modified 12 days ago by genomax64k • written 12 days ago by junghyunshim0

Okay, cool, so, everything is now okay?

ADD REPLYlink written 12 days ago by Kevin Blighe39k

Thanks. it is getting better.

However I can get the list only. How can I get all the matrix according to the list?

I copied and pasted the list to excel and get the matrix data from the original file using v-lookup. It took a while for re-arranging the list from R to one column of excel.

ADD REPLYlink written 12 days ago by junghyunshim0

You mean to re-order the data matrix based on the indices? The indices relate to your original matrix. So, you should be able to do something like:

dat[,out$colInd]
ADD REPLYlink written 12 days ago by Kevin Blighe39k
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