% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/svg.R
\name{PlotCharacterMapping}
\alias{PlotCharacterMapping}
\title{Plot character mapping}
\usage{
PlotCharacterMapping(char, stateLabels, singleTree, legendText,
  SetPar = par(mar = rep(0.2, 4), cex = 0.7), canvas, treeNames,
  analysisLabels = canvas$analysisNames, charIndex = character(0),
  svgFilename = "tree_\%s.svg")
}
\arguments{
\item{char}{Character vector specifying distribution of tokens among (named)
taxa}

\item{stateLabels}{Character vector specifying the labels to apply to each
state}

\item{singleTree}{A single tree to be plotted in Latex output}

\item{legendText}{Character giving legend text to print in Latex output}

\item{SetPar}{Graphical parameters to set before plotting PNG tree
in Latex output.}

\item{canvas}{an object of class SVGForest.}

\item{treeNames}{Character string naming the analysis used to generate each tree}

\item{analysisLabels}{Character vector specifying names of each analysis,
to be printed on plot}

\item{charIndex}{Character vector providing a reference for the character,
typically its number, to be sent to \link{SVGTree}}

\item{svgFilename}{Character string specifying location to save each file,
containing the expression \code{\%s}, which will be replaced with the number
of the tree.}
}
\value{
Prints the tree in an appropriate markdown format
}
\description{
Plot a tree depicting a character reconstruction
}
\details{
This function will plot a reconstruction of the distribution of character \code{char}
on a set of phylogenetic trees.
The function is intended for use in R Markdown (\code{.Rmd}) documents, which might
be rendered using the \code{knitr}, \code{rmarkdown} or \code{bookdown} pacakges.
These packages can produce output in PDF or HTML format; this package will
generate SVG files for HTML output, and a static PNG otherwise.

The SVG output will generate a separate plot for each tree in \code{canvas};
JavaScript can be specified using \link{PrintSwitcher} or \link{PrintJavascript} in order
to allow the user to switch between trees.  Due to the space considerations
implicit in PDF documents, the PNG images include only a single tree,
specified by \code{singleTree}.

HTML output can be forced by setting \code{setOption('localInstance', TRUE)}.
}
\examples{
  # An example is given in the help page for SVGCanvas; type ?SVGCanvas
}
\author{
Martin R. Smith
}