% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plot-genes.R
\name{plotScatter}
\alias{plotScatter}
\title{Gene Expression Scatterplot}
\usage{
plotScatter(
  object,
  label.x,
  label.y,
  label.color = NULL,
  label.x.type = "search",
  label.y.type = "search",
  label.color.type = "search",
  cells = NULL,
  point.size = 1,
  point.alpha = 1,
  xlim = NULL,
  ylim = NULL,
  density.background = T,
  density.color = "#888888",
  density.bandwidth = 1,
  density.bins = 128,
  density.exclude.origin = T,
  xlab = label.x,
  ylab = label.y,
  colorlab = label.color,
  title = "",
  legend = T
)
}
\arguments{
\item{object}{An URD object}

\item{label.x}{(Character) Value to plot on the x-axis}

\item{label.y}{(Character) Value to plot on the y-axis}

\item{label.color}{(Character) Value to plot as point color}

\item{label.x.type}{(Character) Where to look for the label.x; Default is "search" which looks in order: "meta", "group", "sig", "gene", "pseudotime", "pc", "diff.data"}

\item{label.y.type}{(Character) Where to look for the label.y; Default is "search" which looks in order: "meta", "group", "sig", "gene", "pseudotime", "pc", "diff.data"}

\item{label.color.type}{(Character) Where to look for the label.color; Default is "search" which looks in order: "meta", "group", "sig", "gene", "pseudotime", "pc", "diff.data"}

\item{cells}{(Character vector) Names of cells to include in the plot (Default, \code{NULL} is all cells.)}

\item{point.size}{(Numeric) Adjust size of points on the plot}

\item{point.alpha}{(Numeric) Adjust transparency of points on the plot}

\item{xlim}{(Numeric vector) X-axis limits (Default \code{NULL} lets ggplot2 automatically decide.)}

\item{ylim}{(Numeric vector) Y-axis limits (Default \code{NULL} lets ggplot2 automatically decide.)}

\item{density.background}{(Logical) Should}

\item{density.color}{(Character) Darkest color of the density scale}

\item{density.bandwidth}{(Numeric) The kernel bandwidth used in calculating the density background is multiplied by this factor.}

\item{density.bins}{(Numeric) Number of bins to use for 2D kernel estimation.}

\item{density.exclude.origin}{(Logical) Whether values with expression (0,0) should be excluded from the density calculation. (The number of non-expressing cells can often overwhelm the density calculation and make it useless if the genes plotted are specific to a particular lineage and \code{cells} is not used to restrict the cells on the plot.)}

\item{xlab}{(Character) X-axis label}

\item{ylab}{(Character) Y-axis label}

\item{colorlab}{(Character) Color guide label}

\item{title}{(Character) Title of plot}

\item{legend}{(Logical) Display a legend}
}
\description{
Gene Expression Scatterplot
}
