Trees¶

This module provides some facilities for constructing and plotting trees. It is mostly a wrapper around a very limited subset of functions from the R ape package (Analyses of Phylogenetics and Evolution).

R must be installed, the ape R package must be installed, and the Python package rpy2 must be installed, e.g.:

$ apt-get install r-base
$ pip install rpy2
$ R
> install.packages("ape")

See also

anhima.dist.pairwise_distance

anhima.tree.read_tree(filename, **kwargs)[source]¶

Wrapper for the ape read.tree function, which reads a file which contains one or several trees in parenthetic format known as the Newick or New Hampshire format.

Parameters:

filename : string

Name of the file to read.

**kwargs : keyword arguments

All further keyword arguments are passed through to read.tree.

Returns:

tree : R object of class “phylo”

If several trees are read in the file, the returned object is of class “multiPhylo”, and is a list of objects of class “phylo”. The name of each tree can be specified by tree.names, or can be read from the file (see details).

anhima.tree.write_tree(tree, filename=None, **kwargs)[source]¶

Wrapper for the ape write.tree function, which writes in a file a tree in parenthetic format using the Newick (also known as New Hampshire) format.

Parameters:

tree : R object of class “phylo”

The tree to be written.

filename : string, optional

The name of the file to write to. If ommitted, write the file to a string and return it.

**kwargs : keyword arguments

All further keyword arguments are passed through to write.tree.

Returns:

result : string

A string if filename is None, otherwise no return value.

anhima.tree.plot_phylo(tree, plot_kwargs=None, add_scale_bar=None, filename=None, width=None, height=None, units=None, res=None, pointsize=None, bg=None, ax=None, imshow_kwargs=None)[source]¶

Wrapper for the ape plot.phylo function, which plots phylogenetic trees. Plotting will use the R png graphics device.

Parameters:

tree : R object of class “phylo”

The tree to plot.

plot_kwargs : dict-like, optional

A dictionary of keyword arguments that will be passed through to the ape function plot.phylo(). See the documentation for the ape package for a full list of supported arguments.

add_scale_bar : dict-like, optional

A dictionary of keyword arguments that will be passed through to the ape function add.scale.bar(). See the documentation for the ape package for a full list of supported arguments.

filename : string, optional

File path for the generated PNG image. If None, a temporary file will be used.

width : int or float, optional

Width of the plot in units.

height : int or float, optional

Height of the plot in units.

units : {‘px’, ‘in’, ‘cm’, ‘mm’}, optional

The units in which ‘height’ and ‘width’ are given. Can be ‘px’ (pixels, the default), ‘in’ (inches), ‘cm’ or ‘mm’.

res : int, optional

The nominal resolution in ppi which will be recorded in the bitmap file, if a positive integer. Also used for ‘units’ other than the default, and to convert points to pixels.

pointsize : float, optional

The default pointsize of plotted text, interpreted as big points ( 1/72 inch) at ‘res’ ppi.

bg : color, optional

The background color.

ax : axes, optional

The axes on which to draw. If not provided, a new figure will be created.

imshow_kwargs : dict-like

Additional keyword arguments passed through to imshow().

Returns:

ax : axes

The axes on which the plot was drawn.

anhima.tree.color_edges_by_group_majority(tree, labels, groups, colors, equality_color='gray')[source]¶

Color the edges of a tree according to the majority group membership of the descendant tips.

Parameters:

tree : R object of class “phylo”

The tree containing the edges to be colored.

labels : sequence of strings

The tip labels.

groups : sequence of strings

A sequence of strings of the same length as labels, where each item is an identifier for the group to which the corresponding tip belongs.

colors : dict-like

A dictionary mapping groups to colors.

equality_color : string, optional

The color to use in the event of a tie.

Returns:

edge_colors : list of strings

A list of colors for the edges of the tree, to be passed into plot_phylo().