CODEWITHSUNDEEP
rphylogeny
Francisco
Francisco

Reputation: 189

Drawing points in phylogenetic tree R

I would like to draw only one point on the fist node, and then draw another one in the first tip. So far I could draw points but only all of them at once and I cannot find the way to draw it separately. What I have so far:

library(ape)
t3 = '((a:1,b:1):1,(c:1.5,d:0.5):0.5):1;'
plot(read.tree(text = t3),root.edge=T)
nodelabels(pch=21, col="black", adj=1, bg='blue', cex=2)

any help is appreciated

Upvotes: 1

Views: 526

Answers (2)

Torda Varga
Torda Varga

Reputation: 11

You can define to which node you want to plot with the "node" argument within the nodelabels function, and the same is true for tiplabels function but with "tip" argument. So:

library(ape)
t3 = '((a:1,b:1):1,(c:1.5,d:0.5):0.5):1;'
tree <- read.tree(text = t3)
first_node <- length(tree$tip.label)+1
plot(tree, root.edge=T)
nodelabels(node = first_node, pch=21, col="black", bg='blue', cex=2)
tiplabels(tip = 1, pch=21, col="black", bg='blue', cex=2)

Upvotes: 1

kangaroo_cliff
kangaroo_cliff

Reputation: 6222

This isn't the exact answer, but it should help. I got this by looking at the code for nodelabels function. 

library(ape)
t3 = '((a:1,b:1):1,(c:1.5,d:0.5):0.5):1;'
plot(read.tree(text = t3),root.edge=T)

lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
node <- (lastPP$Ntip + 1):length(lastPP$xx)
XX <- lastPP$xx[node]
YY <- lastPP$yy[node]
BOTHlabels(text="", node, XX[1], YY[1], adj = c(0.5, 0.5), 
frame = "rect", pch = 21, thermo = NULL, pie = NULL, 
piecol = NULL, col = "blue", bg = "blue", 
horiz = FALSE, width = NULL, height = NULL, cex=2)

The XX's and YY's gives the nodes. Here, I'm using only the first one. What you have to do for tips is similar, too. Have a look at the code for tiplabels.

Upvotes: 1

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