https://github.com/satijalab/seurat
Tip revision: 7369248c139783ad906aad1f8ca4e6ebab0d004a authored by Andrew Butler on 27 July 2017, 00:52:21 UTC
update version to release 2.0
update version to release 2.0
Tip revision: 7369248
VlnPlot.Rd
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plotting.R
\name{VlnPlot}
\alias{VlnPlot}
\title{Single cell violin plot}
\usage{
VlnPlot(object, features.plot, ident.include = NULL, nCol = NULL,
do.sort = FALSE, y.max = NULL, same.y.lims = FALSE, size.x.use = 16,
size.y.use = 16, size.title.use = 20, adjust.use = 1,
point.size.use = 1, cols.use = NULL, group.by = NULL, y.log = FALSE,
x.lab.rot = FALSE, y.lab.rot = FALSE, legend.position = "right",
single.legend = TRUE, remove.legend = FALSE, do.return = FALSE,
return.plotlist = FALSE, ...)
}
\arguments{
\item{object}{Seurat object}
\item{features.plot}{Features to plot (gene expression, metrics, PC scores,
anything that can be retreived by FetchData)}
\item{ident.include}{Which classes to include in the plot (default is all)}
\item{nCol}{Number of columns if multiple plots are displayed}
\item{do.sort}{Sort identity classes (on the x-axis) by the average
expression of the attribute being potted}
\item{y.max}{Maximum y axis value}
\item{same.y.lims}{Set all the y-axis limits to the same values}
\item{size.x.use}{X axis title font size}
\item{size.y.use}{Y axis title font size}
\item{size.title.use}{Main title font size}
\item{adjust.use}{Adjust parameter for geom_violin}
\item{point.size.use}{Point size for geom_violin}
\item{cols.use}{Colors to use for plotting}
\item{group.by}{Group (color) cells in different ways (for example, orig.ident)}
\item{y.log}{plot Y axis on log scale}
\item{x.lab.rot}{Rotate x-axis labels}
\item{y.lab.rot}{Rotate y-axis labels}
\item{legend.position}{Position the legend for the plot}
\item{single.legend}{Consolidate legend the legend for all plots}
\item{remove.legend}{Remove the legend from the plot}
\item{do.return}{Return a ggplot2 object (default : FALSE)}
\item{return.plotlist}{Return the list of individual plots instead of compiled plot.}
\item{\dots}{additional parameters to pass to FetchData (for example, use.imputed, use.scaled, use.raw)}
}
\value{
By default, no return, only graphical output. If do.return=TRUE,
returns a list of ggplot objects.
}
\description{
Draws a violin plot of single cell data (gene expression, metrics, PC
scores, etc.)
}