Labelling and counting internal nodes of trees using R
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4.1 years ago
Speed.Lee ▴ 30

Hi, I am a student with no biological background but currently, I am working with cladogram (evolutionary theory?) using R.So my apologise in advance if the following questions are too dumb.

What I am using is R with Phangorn and APE. I managed to get the maximum parsimony tree I want, but the labels are only appeared at Leafs. I searched the document of Phangorn but find noting to create labels for the internal nodes automatically.What I want is the nodes presents the characters that made the bifurcation.

My current code for this is:

plot(treePars, show.node.label = TRUE)

Is there any way to get this done? Using other packages are fine.

The second question is when I import data to R as phaDat, it seems automatically transposed. That is, my data is stored in csv file in rows, but when I read it into phaDat, the row names becomes the column heads. My code for this is:

origin <- read.csv(file.choose(),header = TRUE, row.names = 1) events <- as.phyDat(origin, type="USER", levels=c(0,1))

I have tried to transpose data before transform to phyDat, the code for this is:

origin <- read.csv(file.choose(),header = TRUE, row.names = 1) transposed <- t(origin) events <- as.phyDat(transposed, type="USER", levels=c(0,1))

but it is not working. If I transpose data in the csv file directly, it will work. Is there any explanation?

The third question is, is there any method to generate a summary list of the characters at the nodes? e.g. the most ancestral ones marked as level 1s, and the ones directly linked to them as level 2s etc, and get a list of this? If it is possible, also a frequency list for all the characters appeared in the tree? (Sorry, but I have no idea of how to do this so I have no code to present because I am totally stuck with this one.)

Thank you in advance for all comments.

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