how to modify some tiplabs in ggtree?
1
0
Entering edit mode
15 months ago
luzglongoria ▴ 40

Hi there,

I am creating a tree with ggtree and the only thing I am not able to do is to modify some tiplabs (only some! ) in the tree. This is my command:

tree = read.tree(text = "XXXXX;")

p <- ggtree(tree)

## create a data frame that contains the taxa name and the country:
dd <- data.frame(taxa  = c("y","z","d"), 
                 Location = c(rep("here", 2), rep("there", 1)))
row.names(dd) <- NULL
print(dd)

### do the tree (use dev.off())
p <- p %<+% dd + geom_tippoint(aes(color=Location),size=6)
p+theme(legend.position="right")+
  scale_color_brewer("Location", palette="Dark2")+
  geom_tiplab(size=3.5,hjust =-0.1)+
  xlim(NA, 0.15)

I have read that with "geom_tiplab" is posible to change the style of the text but for the whole tree and I don't want that.

Any idea?

Thank you so much

ggtree tree tiplab bold geom_tiplab • 1.2k views
ADD COMMENT
0
Entering edit mode

Were you able to figure this out? I'm looking for an answer to this as well, but to change hjust position for a subset of taxa/tip labels. Please let me know if you figured this out.

ADD REPLY
2
Entering edit mode
6 months ago
andrespara ▴ 30

This might help https://groups.google.com/g/bioc-ggtree/c/Ciy4Fh_7hl4

library(ape)
library(ggtree)

tree <- rcoal(5)
tree$tip.label <- c("REF-1","REF-2","S1","S2","S3")
full_tree    <- ggtree(tree) + xlim(0,2) + geom_tiplab()
full_tree
#Since we know the first two are reference, use the order
limited_tree1 <- ggtree(tree) + xlim(0,2) + geom_tiplab(aes(subset=(node %in% c(1,2))))
limited_tree1
#But we also know the names are different, so we can use that as well
#grepl() searches for 'RE' in the label, and returns true if found
#we use aes(subset=()) to only print those with the subset condition == TRUE
limited_tree2 <- ggtree(tree) + xlim(0,2) + geom_tiplab(aes(
      subset=(grepl('RE',label,fixed=TRUE)==TRUE)))
limited_tree2
ADD COMMENT

Login before adding your answer.

Traffic: 2041 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6