% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plot.algorithm.R
\name{plot.states.matrix}
\alias{plot.states.matrix}
\title{Plot tree and ancestral states}
\usage{
\method{plot}{states.matrix}(x, passes = c(1, 2, 3, 4), show.labels = 0,
  col.tips.nodes = c("#fc8d59", "#eeeeeed0", "#7fbf7be0", "#af8dc3e0"),
  counts = 0, use.edge.length = FALSE, col.states = FALSE,
  state.labels = character(0), legend.pos = "bottomleft", y.lim = NULL,
  ...)
}
\arguments{
\item{x}{A \code{states.matrix} list from \code{\link{apply.reconstruction}}}

\item{passes}{\code{numeric}, the number of passes to plot (default = \code{c(1,2,3,4)}).
Set to 0 to leave nodes unlabelled.}

\item{show.labels}{\code{numeric}, either \code{1} for showing the tip labels, \code{2} for the node labels or \code{c(1,2)} for both (default = \code{NULL}).}

\item{col.tips.nodes}{\code{character}, a vector of up to four colors to be
used for displaying respectively the tips, the nodes,
and (if \code{counts != 0}) the activated/counted nodes
and the nodes at which regions are counted.}

\item{counts}{\code{numeric}, whether to display the activations (\code{1}) or/and the homoplasies (\code{2}) or nothing (\code{0}; default).}

\item{use.edge.length}{\code{logical} indicating whether to use the edge lengths of the phylogeny to draw the branches or not (default).}

\item{col.states}{\code{logical}, whether to colour the states of the tips (\code{TRUE}) or not (\code{FALSE}, default).}

\item{state.labels}{vector of mode \code{character} containing labels for
each state of the character, in order, to be plotted if
col.states is \code{TRUE}.}

\item{legend.pos}{\code{character}, where to position the legend -- e.g. \code{bottomleft}.
Sent as \code{x} parameter to \code{\link{legend}}.
Specify \code{none} to hide the legend.`}

\item{y.lim}{\code{numeric} \emph{x} and \emph{y} coordinates for limits of the plot,
calculated automatically based on presence of legend if set to \code{NULL}
(the default).}

\item{\dots}{any optional arguments to be passed to \code{\link[ape]{plot.phylo}}}
}
\description{
Plots an ancestral states reconstruction and tree score
}
\examples{
## A balanced 12 taxa tree
tree <- ape::read.tree(
                 text = "((((((1,2),3),4),5),6),(7,(8,(9,(10,(11,12))))));")
## A character with inapplicable data
character <- "23--1??--032"

## NA algorithm
NA_matrix <- apply.reconstruction(tree, character, passes = 4, method = "NA")

## Plotting the tree and the states
plot(NA_matrix)

## Plotting the tree and the states with the state changes and regions
plot(NA_matrix, counts = c(1,2))

## Plot the tree with tip/node labels, and only the 1st and 2nd downpass
plot(NA_matrix, passes = c(1,3), show.labels = c(1,2))

## Plot the tree only the 2nd uppass with the state changes in green
plot(NA_matrix, show.labels = 2, col.tips.nodes = c("red", "pink", "green"),
     counts = c(1,2), passes = c(3,4))

}
\seealso{
\code{\link{apply.reconstruction}}, \code{\link{runInapp}}
}
\author{
Thomas Guillerme, Martin R. Smith
}