% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/tree-plots.R
\name{plotTree}
\alias{plotTree}
\title{Plot 2D Dendrogram of URD Tree}
\usage{
plotTree(
  object,
  label = NULL,
  label.type = "search",
  title = label,
  legend = T,
  legend.title = "",
  legend.point.size = 6 * cell.size,
  plot.tree = T,
  tree.alpha = 1,
  tree.size = 1,
  plot.cells = T,
  cell.alpha = 0.25,
  cell.size = 0.5,
  label.x = T,
  label.segments = F,
  discrete.ignore.na = F,
  color.tree = NULL,
  continuous.colors = NULL,
  discrete.colors = NULL,
  color.limits = NULL,
  symmetric.color.scale = NULL,
  hide.y.ticks = T,
  cells.highlight = NULL,
  cells.highlight.alpha = 1,
  cells.highlight.size = 2
)
}
\arguments{
\item{object}{An URD object}

\item{label}{(Character) Data to use for color information, see \link{data.for.plot}}

\item{label.type}{(Character) See \link{data.for.plot}}

\item{title}{(Character) Title to display on the plot}

\item{legend}{(Logical) Show a legend?}

\item{legend.title}{(Character) Title to display on the legend}

\item{legend.point.size}{(Numeric) How big should points be in the legend?}

\item{plot.tree}{(Logical) Whether cells should be plotted with the tree}

\item{tree.alpha}{(Numeric) Transparency of dendrogram (0 is transparent, 1 is opaque)}

\item{tree.size}{(Numeric) Thickness of lines of dendrogram}

\item{cell.alpha}{(Numeric) Transparency of cells (0 is transparent, 1 is opaque)}

\item{cell.size}{(Numeric) How large should cells be}

\item{label.x}{(Logical) Should tips on the x-axis be labeled}

\item{label.segments}{(Logical) Should segments of the dendrogram be labeled with their numbers}

\item{discrete.ignore.na}{(Logical)}

\item{color.tree}{(Logical) Should the dendrogram be colored according to the data? Default \code{NULL} colors the tree when plotting continuous variables, but not when plotting discrete variables.}

\item{continuous.colors}{(Character vector) Colors to make color scale if plotting a continuous variable}

\item{discrete.colors}{(Character vector) Colors to use if plotting a discrete variable}

\item{color.limits}{(Numeric vector, length 2) Minimum and maximum values for color scale. Default \code{NULL} auto-detects.}

\item{symmetric.color.scale}{(Logical) Should the color scale be symmetric and centered around 0? (Default \code{NULL} is \code{FALSE} if all values are positive, and \code{TRUE} if both positive and negative values are present.)}

\item{hide.y.ticks}{(Logical) Should the pseudotime values on the y-axis be hidden?}

\item{cells.highlight}{(Character vector) Group of cells to plot last, ensuring that they are highlighted on the tree.}

\item{cells.highlight.alpha}{(Numeric) Transparency of highlighted cells (0 is transparent, 1 is opaque)}

\item{cells.highlight.size}{(Numeric) Size of highlighted cells}
}
\value{
A ggplot2 object
}
\description{
Plot 2D Dendrogram of URD Tree
}
