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Heatmap.2 dendrogram generation

I used heatmap.2 in R, to create a heatmap. I used the following command :

heatmap.2(as.matrix(mat_data), density.info="none", trace="none", margins =c(12,9), col=my_palette, breaks=seq(96,100,0.5), dendrogram="both")

What is the method used by the heatmap.2 for dendrogram generation? Is it hclust()? If so, what metric (euclidean or manhattan distance) does it use for default, since I have used default parameters in the above command.

heatmap.2 r hclust
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updated by Ram Ram • written by manjumoorthy95 • manjumoorthy95

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written by Ram Ram

1 answer

Please read the manual well. It says

... dendrograms are computed as dd <- as.dendrogram(hclustfun(distfun(X))) where X is either x or t(x).

where distful defaults to stats::dist and hclustfun defaults to stats::hclust.

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written by Ram Ram

Iam sorry, but again what is the metric used by hclust() to find distance as we pass the function from distfun(). Is there any default metric ?

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written by manjumoorthy95 • manjumoorthy95

To get to that, you’ll either need to ask the developer or look into the source code for all instances of hclustfun being used. I’d recommend doing both - the latter approach is great as a learning method.

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written by Ram Ram

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