News of ggtree

December 30, 2015

(This article was first published on R on G. Yu, and kindly contributed to R-bloggers)

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 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.

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