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Here I have code that draw simple phylogenetic tree from newick format:
library(ape)
t<-read.tree(text="(F:4,( (D:2,E:2):1,(C:2,(B:1,A:1):1):1):1);")
plot(t,use.egde.length=TRUE)
i am"displaying" correct length of branches, but i want all branch to have labal with it.
edit:
i want my plot to look like this:
I was searching documentation, but I cannot find method to display length of branch in R. How can i do this ?
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Each height is scaled so that root height is 1, and then raised at power 'rho' (> 0). Branch lengths are then computed as the difference between height of lower node and height of upper node.
Phylogram: Branch lengths are directly related to the amount of genetic change. The longer the branch of a tree, the greater the amount of phylogenetic change that has taken place.
Phylogenetic Systematics Sometimes, e.g., with molecular sequence data, one or more taxa will have a very long branch, meaning that these taxa have a large number of autapomorphies relative to other taxa in the analysis (e.g., taxon Z of Figure 2.14D).
Unless indicated otherwise, a phylogenetic tree only depicts the branching history of common ancestry. The pattern of branching (i.e., the topology) is what matters here. Branch lengths are irrelevant--they are simply drawn in whatever way makes the tree look most tidy.
You can do it by extracting edge lengths and using edgelabels().
# Load package
library(ape)
# Create data
t <- read.tree(text="(F:4,((D:2,E:2):1,(C:2,(B:1,A:1):1):1):1);")
plot(t)
edgelabels(t$edge.length, bg="black", col="white", font=2)
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