ggphylo: Plots a tree or a list of trees using 'ggplot'.

In gjuggler/ggphylo: Tools for laying out and plotting phylogenetic data (trees and alignments) with ggplot.

Description

Plots a tree or a list of trees using ggplot.

ggphylo provides convenient functions and tools for visualizing phylogenetic data in R. Many methods are provided to simplify the process of working with phylo objects (e.g., tree.scale.to and tree.translate , while two plotting methods allow for a wide range of expressive plots: tree.plot and aln.plot

Usage

  ggphylo(x, extra.data = NA, layout = "default",
    do.plot = T, facet.trees = T, x.lab = "Branch Length",
    x.lim = NA, x.expand = c(0.05, 0.3), y.lim = NA, ...)

Arguments

x	input phylo object, list of phylo objects, or a Newick- or NHX-format tree string. When a list is given, all trees will be arranged using facet_wrap into a grid of plots. Trees of different shapes and sizes can be included; the plotting area will be expanded to fit the largest input tree.
extra.data	an optional data.frame or string pointing to a CSV file, containing data to be linked to the input phylo object(s). The input data must contain a column named 'label', which will be used to match each row in the data to a node in the input tree(s). Defaults to NA.
layout	a string indicating how the tree will be laid out. Defaults to 'defualt'. Available layouts include: default The 'default' layout, which arranges the tree in the standard 'phylogram' arrangement with branch length along the x-axis and tree nodes evenly spaced along the y-axis. unrooted The 'unrooted' layout, which arranges the tree from root-to-tip giving equal viewing angle to each clade according to its size. radial The 'radial' layout, which is equivalent to the 'default' layout but plotted in polar coordinates.
do.plot	a boolean indicating whether the plot should be printed to the current graphics device. When FALSE, the plot is not printed; the graphics grob is silently returned. Defaults to TRUE.
plot.internals	boolean, whether the labels of internal nodes should be shown. Defaults to FALSE.
x.lab	string, the label given to the x-axis (or, when layout='unrooted', given to both axes). Defaults to 'Branch Length'.
x.lim	vector of length 2, the lower and upper limits to apply to the x-axis. Defaults to NA, in which case the plot is expanded to include the entire tree.
y.lim	vector of length 2, the lower and upper limits to apply to the y-axis. Defaults to NA, in which case the plot is expanded to include the entire tree.
x.expand	vector of length 2, the fraction by which to expand the x-axis limits to the left and to the right. This is useful to allow extra space for trees with long labels or large node sizes. Defaults to c(0.05, 0.3) which extends the x-axis limits 5 the right of the default size.
[line|node|label].[size|color|alpha].by	string, indicating the name of a tag value by which to modulate the given visual property. A value of 0 will be given to nodes which do not contain the given tag, and unless a 'x.y.scale' parameter is given (see below), the default ggplot scaling and size/color/alpha rules will be applied. The combination of 3 visual elements and 3 visual properties creates 9 possible parameters to choose from: line.size.by line.color.by line.alpha.by node.size.by node.color.by node.alpha.by label.size.by label.color.by label.alpha.by
[line|node|label].[size|color|alpha].scale	function, used in conjunction with a corresponding 'x.y.by' parameter (e.g. node.scale.by) to specify the type, limits and range of the visual scaling. The value is usually the result of one of the ggplot scale convenience functions, such as: node.size.scale=scale_size_continuous(limits=c(0,100), range=c(1, 5)) In this example, 'limits' controls the range of tag values to be shown, and 'range' controls the range of the resulting visual scale (i.e. the node size will range from 1 to 5). See scale_size_continuous or the other ggplot scale_x_y functions for more info.
[line|node|label].[size|color|alpha]	string or numeric, used to specify a constant value for a visual parameter if no data-based scaling is specified. Default values are: line.size 1 line.color '#888888' line.alpha 1 node.size 1.5 node.color '#333333' node.alpha 1 label.size 3 label.color 'black' label.alpha 1

Value

the ggplot grob list.

gjuggler/ggphylo documentation built on May 17, 2019, 6:05 a.m.