dotTree

dot.legend

tree

vector of trait values; or a matrix. In the case of <code>dot.legend</code>, the <em>x</em> coordinate of the legend.

logical value indicating whether or not a legend should be plotted.

legend

tree plotting method to be used internally. Will switch to <code>method="phylogram"</code> if the number of traits is greater than one. For <code>dot.legend</code>, it should be the method that was used for the plot.

method

a logical value indicating whether or not to standardize <code>x</code>, or each column of <code>x</code>, to have a mean of zero & variance of one prior to analysis.

standardize

minimum value for <code>dot.legend</code>.

maximum value for <code>dot.legend</code>.

number of tips in the plotted tree for <code>dot.legend</code>.

Ntip

length

logical value indicating whether or not to prompt for legend position.

prompt

optional arguments. In the case of <code>dotTree</code>, these will be passed to <code><a rd-options="" href="/link/plotTree?package=phytools&version=0.5-38" data-mini-rdoc="phytools::plotTree">plotTree</a></code> or a different internally used plotting function for <code>method="phylogram"</code>. See <code><a rd-options="" href="/link/phylo.heatmap?package=phytools&version=0.5-38" data-mini-rdoc="phytools::phylo.heatmap">phylo.heatmap</a></code> for more detail on these arguments. Other option for <code>dotTree</code> also include <code>data.type</code> (<code>"continuous"</code> or <code>"discrete"</code>), <code>colors</code>, <code>length</code>, for data type <code>"continuous"</code> the length of the legend in terms of plotted circles, <code>x.space</code>, the spacing of the columns in the plotted data matrix, and <code>leg.space</code>, the spacing of the legend dots (again, for <code>data.type="continuous"</code> only).


	Creates a plot in which different sized dots/circles represent different tip values for a quantitative trait.


phylogenetics

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; and fitting a model in which a discrete
character evolves under the threshold model. 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; 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)

dotTree function

optional arguments. In the case of <code>dotTree</code>, these will be passed to <code><a rd-options='' href='plotTree'>plotTree</a></code> or a different internally used plotting function for <code>method="phylogram"</code>. See <code><a rd-options='' href='phylo.heatmap'>phylo.heatmap</a></code> for more detail on these arguments. Other option for <code>dotTree</code> also include <code>data.type</code> (<code>"continuous"</code> or <code>"discrete"</code>), <code>colors</code>, <code>length</code>, for data type <code>"continuous"</code> the length of the legend in terms of plotted circles, <code>x.space</code>, the spacing of the columns in the plotted data matrix, and <code>leg.space</code>, the spacing of the legend dots (again, for <code>data.type="continuous"</code> only).

dotTree: Creates a phylogenetic dot plot

Description

Usage

Arguments

Value

References