Question: Problem with font size in a tree
gravatar for luzglongoria
11 months ago by
luzglongoria40 wrote:


I am trying to make an interaction between two phylogenetic trees. I am able to run all the code (no errors) the problem is that the size of the letter of one of the trees is too big enter image description here

I have been able to change the size by plotting the plot and asking R to minimize the size but the problem is that I want to use the tree for an interaction with another tree. Please, see below:

# Packages

 #Import trees
bTreeH = read.newick(file="Huanuco_bird_tree.newick")
pTreeH ="Huanuco_parasite_tree.nex")

# Prepare parasite Tree
  pTreeH = force.ultrametric(pTreeH)

# Create two fata frames

df.bird.H = data.frame(name = c("Amazilia_chionogaster",

  df.parasite.H = data.frame(Name = c("P_SGS1",

# Creation of the association matrix:
  associationH <- cbind(df.bird.H, df.parasite.H)

# Create a vector for colors
  cols.H <- c('2','1','2','2','1','2','1','1','1','1','2','1')

# Create a vector for chose colors
  cols.1.H <- c("#e7298a","grey","#e7298a","#e7298a","grey","#e7298a","grey","grey","grey","grey","#e7298a","grey")  #1

# Create the two trees face to face
  Interaction_Huanuco <- cophyloplot(bTreeH, pTreeH, assoc=associationH,
                   length.line = 4, space = 100, gap = 3, col = cols.1.H)

There is no error message but the bTreeH (the one with more names) is imposible to read properly because of the size of the letters. Some months ago I was able to run these analyses with any trouble, the size of the letters seemed to adjust itself but now... I am running exactly the same code and I have this problem.

Any help is more than welcome.

ADD COMMENTlink modified 9 months ago by tiffany.chin20 • written 11 months ago by luzglongoria40
gravatar for tiffany.chin
9 months ago by
tiffany.chin20 wrote:

I had the same problem; see:

I wasn't able to copy the internal function as mentioned in the above link, but I found a work around.

You'll have to edit the internal function plotCophylo2 to change the text size with cex: (where the function refers to text, cex = 1; change to cex = 0.5).

In my case, I just called the internal function a different name, changed the code for text size, and then fix(cophyloplot) to recall the new internal function. After that, it ran smoothly.

Hope that helps.

ADD COMMENTlink written 9 months ago by tiffany.chin20
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