CODEWITHSUNDEEP
r
Colin
Colin

Reputation: 10820

How do I change the clustering algorithm for heatmap.2 function in R?

I want to change the clustering method that heatmap.2 uses for the hierarchical clustering. It uses hclust by default, which I want to keep using, but hclust uses the "complete" method and I want to do "average". Heatmap.2 has an hclustfun parameter, but I can't figure out how to use it. I tried

heatmap.2(..., hclustfun=hclust(method="average"))

but it gave an error that the 'd' argument is required. Heatmap.2 does it's own distance calculation that can be specified with the distfun parameter. I'm not sure how to somehow pass the distances to hclust, or how else to specify a parameter to be passed to hclust.

Upvotes: 1

Views: 1149

Answers (1)

Julius Vainora
Julius Vainora

Reputation: 48211

You are really close. As hclustfun needs to be a function, the parameter value should indeed be a function, while hclust(method = "average") is calling hclust without specifying d. Meanwhile,

heatmap.2(x, hclustfun = function(d) hclust(d, method = "average"))

works.

Upvotes: 1

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