CODEWITHSUNDEEP
r
user3236841
user3236841

Reputation: 1258

R: display clustered heatmap with simlarity matrix

I have a simlarity matrix as follows:

xx <- cor(matrix(rnorm(650), ncol =25))

I want to cluster this similarity matrix and image in a heatmap. Is the following correct?

yy <- heatmap(1-xx,  Rowv=T, scale='none',symm = T,keep.dendro=F,

Here, I am taking 1-xx which is a dissimilarity matrix. Is this the right thing to do, or should it be input in some other way?

Upvotes: 2

Views: 590

Answers (1)

user3236841
user3236841

Reputation: 1258

I have figured it out upon reading one of the examples in R. Here is what one has to do using the similarity matrix.

hU <- heatmap(xx, Rowv = FALSE, symm = TRUE, 
              distfun = function(c) as.dist(1 - c),
              hclustfun = function(d) hclust(d, method = "single"),
              keep.dendro = FALSE)

I hope that this helps someone!

Upvotes: 1

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