News of ggtree

[This article was first published on R on G. Yu, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here)
Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.

A new version of ggtree that works with ggplot2 (version >= 2.0.0) is now availabel.

new layers

Some functions, add_legend, hilight, annotation_clade and annotation_clade2 were removed. Instead we provide layer functions, geom_treescale, geom_hilight and geom_cladelabel. You can use + operator to add layers using these layer functions.

In addtion, we provide geom_point2, geom_text2 and geom_segment2 which works exactly as geom_point, geom_text and geom_segment except they allow ggtree users do subsetting.

rescale tree

Most of the phylogenetic trees are scaled by evolutionary distance (substitution/site), in ggtree we can re-scale a phylogenetic tree by any numerical variable inferred by evolutionary analysis. For example using substitution rate to scale a time-scaled tree inferred by BEAST, or using dN/dS to re-scale a tree analyzed by CodeML.

New Hampshire eXtended format (NHX) supported

This is a feature request from ggtree user. The NHX format is also commonly used in phylogenetic software (e.g. PHYLODOG, RevBayes, etc).

The original vignette was too long and I split them into several short ones. These vignettes should be more easy to follow. You can access the vignette via http://guangchuangyu.github.io/ggtree/. More examples and detail explanation were provided. If there are something that I didn’t explain well, please don’t hesitate to let me know. I will appreciate your help in improving the ggtree vignettes.

To leave a comment for the author, please follow the link and comment on their blog: R on G. Yu.

R-bloggers.com offers daily e-mail updates about R news and tutorials about learning R and many other topics. Click here if you're looking to post or find an R/data-science job.
Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.

Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)

Click here to close (This popup will not appear again)