DoHeatmap.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plotting.R
\name{DoHeatmap}
\alias{DoHeatmap}
\title{Gene expression heatmap}
\usage{
DoHeatmap(object, data.use = NULL, use.scaled = TRUE, cells.use = NULL,
  genes.use = NULL, disp.min = -2.5, disp.max = 2.5, group.by = "ident",
  draw.line = TRUE, col.low = "#FF00FF", col.mid = "#000000",
  col.high = "#FFFF00", slim.col.label = FALSE, remove.key = FALSE,
  rotate.key = FALSE, title = NULL, cex.col = 10, cex.row = 10,
  group.label.loc = "bottom", group.label.rot = FALSE, group.cex = 15,
  group.spacing = 0.15, assay.type = "RNA", do.plot = TRUE)
}
\arguments{
\item{object}{Seurat object}

\item{data.use}{Option to pass in data to use in the heatmap. Default will pick from either
object@data or object@scale.data depending on use.scaled parameter. Should have cells as columns
and genes as rows.}

\item{use.scaled}{Whether to use the data or scaled data if data.use is NULL}

\item{cells.use}{Cells to include in the heatmap (default is all cells)}

\item{genes.use}{Genes to include in the heatmap (ordered)}

\item{disp.min}{Minimum display value (all values below are clipped)}

\item{disp.max}{Maximum display value (all values above are clipped)}

\item{group.by}{Groups cells by this variable. Default is object@ident}

\item{draw.line}{Draw vertical lines delineating different groups}

\item{col.low}{Color for lowest expression value}

\item{col.mid}{Color for mid expression value}

\item{col.high}{Color for highest expression value}

\item{slim.col.label}{display only the identity class name once for each group}

\item{remove.key}{Removes the color key from the plot.}

\item{rotate.key}{Rotate color scale horizantally}

\item{title}{Title for plot}

\item{cex.col}{Controls size of column labels (cells)}

\item{cex.row}{Controls size of row labels (genes)}

\item{group.label.loc}{Place group labels on bottom or top of plot.}

\item{group.label.rot}{Whether to rotate the group label.}

\item{group.cex}{Size of group label text}

\item{group.spacing}{Controls amount of space between columns.}

\item{assay.type}{to plot heatmap for (default is RNA)}

\item{do.plot}{Whether to display the plot.}
}
\value{
Returns a ggplot2 plot object
}
\description{
Draws a heatmap of single cell gene expression using ggplot2.
}
\examples{
DoHeatmap(object = pbmc_small)

}