plotTree.wBars

plotTree.barplot

plotTree.boxplot

tree

a named vector of trait values. For <code>plotTree.boxplot</code>, the names should repeat for multiple observations per species. For <code>plotTree.boxplot</code> <code>x</code> can also be supplied as a formula, though in that case the factor levels need to be provided in a valid cladewise order of the tips in <code>tree</code>. This order doesn't need to correspond with the current order of the tip labels.

scaling factor for the tip bars (relative to the total tree height).

scale

width

plot type. Can be <code>"phylogram"</code> or <code>"fan"</code>.

type

plotting method to use. Can be <code>"plotTree"</code> (for <code><a rd-options="" href="/link/plotTree?package=phytools&version=0.5-64" data-mini-rdoc="phytools::plotTree">plotTree</a></code>) or <code>"plotSimmap"</code> (for <code><a rd-options="" href="/link/plotSimmap?package=phytools&version=0.5-64" data-mini-rdoc="phytools::plotSimmap">plotSimmap</a></code>).

method

argument indicating whether or not tip labels should be plotted. Defaults to <code>tip.labels=FALSE</code>.

tip.labels

colors of the plotted bars. Can be a single value or a vector with length equal to the number of tips in the tree.

single value specifying the color of the border for the plotted bars. Defaults to <code>border=NULL</code>, which means that black borders will be plotted.

border

in <code>plotTree.barplot</code>, arguments to be passed to <code><a rd-options="" href="/link/plotTree?package=phytools&version=0.5-64" data-mini-rdoc="phytools::plotTree">plotTree</a></code>.

args.plotTree

in <code>plotTree.barplot</code>, arguments to be passed to <code><a rd-options="" href="/link/barplot?package=phytools&version=0.5-64" data-mini-rdoc="phytools::barplot">barplot</a></code>.

args.barplot

in <code>plotTree.boxplot</code>, arguments to be passed to <code><a rd-options="" href="/link/boxplot?package=phytools&version=0.5-64" data-mini-rdoc="phytools::boxplot">boxplot</a></code>.

args.boxplot

optional arguments to be passed to <code><a rd-options="" href="/link/plotTree?package=phytools&version=0.5-64" data-mini-rdoc="phytools::plotTree">plotTree</a></code> or <code><a rd-options="" href="/link/plotSimmap?package=phytools&version=0.5-64" data-mini-rdoc="phytools::plotSimmap">plotSimmap</a></code>.


	<code>plotTree.wbars</code> plots a phylogeny in phylogram or fan style with bars at the tips representing the values for a phenotypic trait.
	
	<code>plotTree.barplot</code> creates a split plot in which a right-facing phylogram is on the left, and a bar plot is shown on the right.
	
	<code>plotTree.boxplot</code> creates a split plot in which a right-facing phylogram is on the left, and a box plot is shown on the right.


phylogenetics

comparative method

plotting

Package contains various functions for phylogenetic analysis.
This functionality is concentrated in the phylogenetic analysis of
comparative data from species. For example, the package includes
functions for Bayesian and ML ancestral state estimation; visual
simulation of trait evolution; fitting models of trait evolution
with multiple Brownian rates and correlations; visualizing
discrete and continuous character evolution using colors or
projections into trait space; identifying the location of a change
in the rate of character evolution on the tree; fast Brownian motion
simulation and simulation under several other models of
continuous trait evolution; fitting a model of correlated binary
trait evolution; locating the position of a fossil or an recently
extinct lineage on a tree using continuous character data with ML;
plotting lineage accumulation through time, including across
multiple trees (such as a Bayesian posterior sample); conducting
an analysis called stochastic character mapping, in which character
histories for a discrete trait are sampled from their posterior
probability distribution under a model; conducting a multiple
(i.e., partial) Mantel test; fitting a phylogenetic regression model
with error in predictor and response variables; conducting a
phylogenetic principal components analysis, a phylogenetic
regression, a reduced major axis regression, a phylogenetic
canonical correlation analysis, and a phylogenetic ANOVA; projecting
a tree onto a geographic map; simulating discrete character
histories on the tree; fitting a model in which a discrete character
evolves under the threshold model; visualization of cospeciation; a
simple statistical test for cospeciation between two trees. In
addition to this phylogenetic comparative method functionality, the
package also contains functions for a wide range of other purposes in
phylogenetic biology. For instance, functionality in this package
includes (but is not restricted to): adding taxa to a tree
(including randomly, everywhere, or automatically to genera);
generating all bi- and multi-furcating trees for a set of taxa;
reducing a phylogeny to its backbone tree; dropping tips or adding
tips to special types of phylogenetic trees; exporting a tree as an
XML file; converting a tree with a mapped character to a tree with
singleton nodes and one character state per edge; estimating a
phylogeny using the least squares method; simulating birth-death
trees under a range of conditions; rerooting trees; computing a
consensus tree under multiple methods, including via minimization
of the distance to other trees in the set; a wide range of
visualizations of trees; and a variety of other manipulations and
analyses that phylogenetic biologists may find useful for their
research.

Liam Revell

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

plotTree.wBars function

plotting method to use. Can be <code>"plotTree"</code> (for <code><a rd-options='' href='plotTree'>plotTree</a></code>) or <code>"plotSimmap"</code> (for <code><a rd-options='' href='plotSimmap'>plotSimmap</a></code>).

in <code>plotTree.barplot</code>, arguments to be passed to <code><a rd-options='' href='plotTree'>plotTree</a></code>.

in <code>plotTree.barplot</code>, arguments to be passed to <code><a rd-options='' href='barplot'>barplot</a></code>.

in <code>plotTree.boxplot</code>, arguments to be passed to <code><a rd-options='' href='boxplot'>boxplot</a></code>.

optional arguments to be passed to <code><a rd-options='' href='plotTree'>plotTree</a></code> or <code><a rd-options='' href='plotSimmap'>plotSimmap</a></code>.

plotTree.wBars: Plot a tree with bars at the tips

Description

Usage

Arguments

Value

References

See Also