Changing branch length of outgroup

[Ollie White]

Hello all, 

When I plot some data using ggtree, the out groups are on a very long branch length. The out groups are 75 and 76 in the example below. 

I would like to keep the out groups in the tree but ignore their branch lengths to make presentation easier.

When I collapse the nodes 75 and 76 it does improve the appearance. but the out groups are still on a long branch.

Is it possible to produce a plot such as the one I created manually below where the branch lengths for the out groups is ignored 

The script I have used so far is below and example data attached. Any thoughts would be much appreciated

Cheers

Ollie

library(ggtree)

# read in data

x <- read.tree("long-branch-example.newick")

# create ggtree object

tree <- ggtree(x) + geom_tiplab(size = 2)

# plot tree

tree

# find node for outgroup

MRCA(x, tip =c("75", "76"))

# collapse outgroup node

tree <- collapse(tree, node = 151)

# plot resulting tree

tree

[Ollie White]

Apologies file attached now

[Yu, Guangchuang]

You can use groupClade to group the 151 clade and use that info to set the linetype. For shortening 75 and 76, you can manipulate their x position.

library(ggtree)
x <- read.tree("long-branch-example.newick")
groupClade(x, 151) -> y
ggtree(y, aes(linetype=group)) + geom_tiplab(size = 2) -> p
p$data[tree$data$node %in% c(75, 76), "x"] = mean(p$data$x)
print(p)

​

--
G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data, Methods in Ecology and Evolution, 2017, 8(1):28-36. doi:10.1111/2041-210X.12628
 
Homepage: https://guangchuangyu.github.io/ggtree
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--

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Guangchuang Yu PhD

Postdoc researcher
State Key Laboratory of Emerging Infectious Diseases
School of Public Health
The University of Hong Kong

Hong Kong SAR, China

www: https://guangchuangyu.github.io

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[Yu, Guangchuang]

Sorry for typo. pls use the following code:

library(ggtree)
x <- read.tree("long-branch-example.newick")
groupClade(x, 151) -> y
ggtree(y, aes(linetype=group)) + geom_tiplab(size = 2

) -> p
p$data[p$data$node %in% c(75, 76), "x"] = mean(p$data$x)
print(p)

​