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$height)/1.5); mycolhc <- rainbow(length(unique(mycl)), start=0.1, end=0.9); mycolhc <- mycolhc[as.vector(mycl)] ; myheatcol <- bluered(75)
One can ofcourse plot the clusters as follows,
`heatmap.2(y, Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc), col=myheatcol, scale="row", density.info="none", trace="none", RowSideColors=mycolhc,margins=c(10,10))'
however, I'd like
geom_tile type of visualization. I have two questions in this regard.
- How can I plot the clusters? I know the order of the genes are in
hr$order. How can I get this to the same order for ggplot?
- Is it also possible to get the dendogram for rowV and colV
Any help would be really great. Thanks!