## convert graphic object to tree object using treeio

I have splitted ggtree to 2 packages, treeio and ggtree. Now ggtree is mainly focus on visualization and annotation, while treeio focus on parsing and exporting tree files. Here is a welcome message from treeio that you can convert ggtree output to tree object which can be exported as newick or nexus file if you want.

Thanks to ggplot2, output of ggtree is actually a ggplot object. The ggtree object can be rendered as graph by print method, but internally it is an object that contains data. treeio defines as.phylo and as.treedata to convert ggtree object to phylo or treedata object.

## add layer to specific panel of facet_plot output

This is a question from ggtree google group:

Dear ggtree team,

how can I apply a geom_xxx to only one facet panel? For example if i want to get geom_hline(yintersect=1:30) or a geom_text() in the dot panel? I cant see the facet_grid(. ~ var) function call, so I don’t know which subsetting to use. I have already read http://stackoverflow.com/questions/29873155/geom-text-and-facets-not-working

  tr <- rtree(30)

d1 <- data.frame(id=tr$tip.label, val=rnorm(30, sd=3)) p <- ggtree(tr) p2 <- facet_plot(p, panel="dot", data=d1, geom=geom_point, aes(x=val), color='firebrick') d2 <- data.frame(id=tr$tip.label, value = abs(rnorm(30, mean=100, sd=50)))

p3 <- facet_plot(p2, panel='bar', data=d2, geom=geom_segment, aes(x=0, xend=value, y=y, yend=y), size=3, color='steelblue') + theme_tree2()


Thanks! Andreas

If this can be done, we can create even more comprehensive tree plots.

## ggtree version of plotTree

PLOTTING TREES + DATA is difficult. @DrKatHolt developed plotTree (R and Python scripts) to visualize associated data with trees, e.g. heatmap, horizontal bar etc.

I reproduced the examples presented in the plotTree repo using ggtree. Source code is freely available in https://github.com/GuangchuangYu/plotTree-ggtree.

Here are the outputs produced by ggtree:

## Edge coloring with user data

Coloring edges in ggtree is quite easy, as we can map the color to numerical or categorical values via the aes(color=VAR) syntax. For user’s own data, it is also easy as ggtree provide the %<+% operator to attach user data.

But as it seems not so obviously for ggtree users, see question 1, 2, and 3, I will demonstrate how to color edges using user data here.

## align genomic features with phylogenetic tree

A question on biostars asking how to generate the following figure:

This can be quite easy to implement in ggtree, I can write a geom layer to layout the alignment. As ggbio already provides many geom for genomic data and I don’t want to re-invent the wheel, I decided to try ggtree+ggbio. This is also the beauty of R that packages complete each others.

## xlim_tree: set x axis limits for only Tree panel

A ggtree user recently asked me the following question in google group:

I try to plot long tip labels in ggtree and usually adjust them using xlim(), however when creating a facet_plot xlim affects all plots and minimizes them.

Is it possible to work around this and only affect the tree and it’s tip labels leaving the other plots in facet_plot unaffected?

This is indeed a desire feature, as ggplot2 can’t automatically adjust xlim for text since the units are in two different spaces (data and pixel).

## facet_plot: a general solution to associate data with phylogenetic tree

ggtree provides gheatmap for visualizing heatmap and msaplot for visualizing multiple sequence alignment with phylogenetic tree.

We may have different data types and want to visualize and align them with the tree. For example, dotplot of SNP site (e.g. using geom_point(shape='|')), barplot of trait values (e.g. using geom_barh(stat='identity')) et al.

To make it easy to associate different types of data with phylogenetic tree, I implemented the facet_plot function which accepts a geom function to draw the input data.frame and display it in an additional panel.

## [Bioc 34] NEWS of my BioC packages

I have 7 packages published within the Bioconductor project.

A new package meshes was included in BioC 3.4 release.

## reproducible logo generated by ggtree

ggtree provides many helper functions for manupulating phylogenetic trees and make it easy to explore tree structure visually.

Here, as examples, I used ggtree to draw capital character G and C, which are first letter of my name :-).

To draw a tree in such shape, we need fan layout (circular layout with open angle) and then rotating the tree to let the open space on the correct position. Here are the source codes to produce the G and C shapes of tree. I am thinking about using the G shaped tree as ggtree logo. Have fun with ggtree :-)

## ggtree for outbreak data

OutbreakTools implements basic tools for the analysis of Disease Outbreaks.

It defines S4 class obkData to store case-base outbreak data. It also provides a function, plotggphy, to visualize such data on the phylogenetic tree.

library(OutbreakTools)
data(FluH1N1pdm2009)
attach(FluH1N1pdm2009)

x <- new("obkData", individuals = individuals, dna = FluH1N1pdm2009$dna, dna.individualID = samples$individualID, dna.date = samples$date, trees = FluH1N1pdm2009$trees)

plotggphy(x, ladderize = TRUE, branch.unit = "year",
tip.color = "location", tip.size = 3, tip.alpha = 0.75)