search for: hc2newick

Hi R helpers... I am having troubles because of the discrepancy between the dendrogram plotted from hclust and what is wrote in the hc2Newick file. I've got a matrix C: > hc <- hclust(dist(C)) > plot(hc) with the: > write(hc2Newick(hc),file='test.newick') both things draw completely different "trees"... I have also tried with the raw distance matrix D and also the agnes function, but the same happ...

Hi, I'm doing hierarchical clustering, and want to export my dendrogram to a tree-viewing/editing software. I can do this by converting the data to Newick format (hc2Newick in ctc package), but I can't get branch lengths to show in the resulting phylogram. I figured it might help to convert my hclust object into a phylo object (as.phylo in ape package), but the following lines give me this "Error in UseMethod("as.phylo") : no applicable method for &...

Dear R-helpers, I would like to export hierarchical clusters e.g. fit <- hclust(d, method="ward") in the newick format write(hc2Newick(fit),file='hclust.newick') Searching for a possibility I found this solution in the package ctc (http://www.bioconductor.org/packages/bioc/html/ctc.html). However, neither from this site nor via CRAN it is possible to install the package. Is there any other possibility? Is the package inc...