I am currently using R with phangorn and ape to create trees because what I use is binary data. My data is like the one shown in the first figure attached.
What I want to get is trees with information as shown in the second figure attached.
The leafs, as well as all internal nodes(or edges), labelled. The label of internal nodes/edges are the characters/ variable names.
How can I do this? Thanks in advance for the comments.
I have a simple solution for you.
1. Recode "yes" as 1 and "no" as 0.
2. Use the heatmap.2 function in R to generate a hierarchically clustered heatmap using your X and Y variables. Keep the dendrogram option on so that a dendrogram is generated as part of the heatmap.
3. If you want the dendrogram without the heatmap, then you can use the class "dendrogram" in R. https://stat.ethz.ch/R-manual/R-devel/library/stats/html/dendrogram.html
This is the fastest method I can think of; it shouldn't take you more than 1 hour tops.
Mohsin
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