Question: Gene Expression Data Hierarchical Clustering, Plot Heat Map With Ggplot
1
gravatar for k.nirmalraman
5.9 years ago by
k.nirmalraman980
Germany
k.nirmalraman980 wrote:

I have expression data, filtered based on DE analysis.

I would like to do hierachical clustering.

y<-ExpressionMatrix_filtered   # n*4 matrix with rownames=genenames
hr <- hclust(as.dist(1-cor(t(y), method="pearson")), method="centroid"); 
hc <- hclust(as.dist(1-cor(y, method="spearman")), method="centroid")  
# Cuts the tree and creates color vector for clusters.
mycl <- cutree(hr,k=4, h=max(hr$height)/1.5); 
mycolhc <- rainbow(length(unique(mycl)), start=0.1, end=0.9); mycolhc <- mycolhc[as.vector(mycl)] ; myheatcol <- bluered(75)

One can ofcourse plot the clusters as follows,

`heatmap.2(y, Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc), col=myheatcol, scale="row", density.info="none", trace="none", RowSideColors=mycolhc,margins=c(10,10))'

however, I'd like ggplot package geom_tile type of visualization. I have two questions in this regard.

  1. How can I plot the clusters? I know the order of the genes are in hr$order. How can I get this to the same order for ggplot?
  2. Is it also possible to get the dendogram for rowV and colV

Any help would be really great. Thanks!

clustering heatmap • 8.4k views
ADD COMMENTlink modified 5.9 years ago by Neilfws48k • written 5.9 years ago by k.nirmalraman980
3
gravatar for Neilfws
5.9 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

These may be useful:

ADD COMMENTlink written 5.9 years ago by Neilfws48k
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