Question: How to cluster in heatmap.2
0
gravatar for Björn
19 months ago by
Björn40
Björn40 wrote:

How to cluster heatmap using different distance matrix (Manhattan or Euclidean) and split column or row-wise in following command

heatmap.2(lcpm, Colv=FALSE, dendrogram="row",labRow = y2$genes$genes, Rowv = TRUE,  col=rev(morecols(20)),trace="none",tracecol = "black",main="Top 20 variable genes across samples",cex.main=0.6, ColSideColors=group.col,scale="row",margins=c(10,9))

Thanks

ADD COMMENTlink modified 19 months ago by Kevin Blighe49k • written 19 months ago by Björn40
6
gravatar for Kevin Blighe
19 months ago by
Kevin Blighe49k
Kevin Blighe49k wrote:

I give an answer here, that indirectly answers your question: A: Heatmap based with FPKM values

In a nutshell, just add the following as parameters to heatmap.2():

#Euclidean distance with Ward's linkage
heatmap.2(
  ...,
  distfun = function(x) dist(x, method="euclidean"),
  hclustfun = function(x) hclust(x, method="ward.D2"))

#1 minus Pearson correlation distance with average linkage
heatmap.2(
  ...,
  distfun = function(x) as.dist(1-cor(t(x))),
  hclustfun = function(x) hclust(x, method="average"))

et cetera

ADD COMMENTlink modified 10 weeks ago • written 19 months ago by Kevin Blighe49k
1

@Kevin Blighe, Thanks, It worked

ADD REPLYlink written 19 months ago by Björn40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1006 users visited in the last hour