https://github.com/satijalab/seurat
Tip revision: c54e57d3423b3f711ccd463e14965cc8de86c31b authored by David Collins on 19 March 2024, 12:18:35 UTC
Merge pull request #8638 from satijalab/develop
Merge pull request #8638 from satijalab/develop
Tip revision: c54e57d
VlnPlot.Rd
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/visualization.R
\name{VlnPlot}
\alias{VlnPlot}
\title{Single cell violin plot}
\usage{
VlnPlot(
object,
features,
cols = NULL,
pt.size = NULL,
alpha = 1,
idents = NULL,
sort = FALSE,
assay = NULL,
group.by = NULL,
split.by = NULL,
adjust = 1,
y.max = NULL,
same.y.lims = FALSE,
log = FALSE,
ncol = NULL,
slot = deprecated(),
layer = NULL,
split.plot = FALSE,
stack = FALSE,
combine = TRUE,
fill.by = "feature",
flip = FALSE,
add.noise = TRUE,
raster = NULL
)
}
\arguments{
\item{object}{Seurat object}
\item{features}{Features to plot (gene expression, metrics, PC scores,
anything that can be retreived by FetchData)}
\item{cols}{Colors to use for plotting}
\item{pt.size}{Point size for points}
\item{alpha}{Alpha value for points}
\item{idents}{Which classes to include in the plot (default is all)}
\item{sort}{Sort identity classes (on the x-axis) by the average
expression of the attribute being potted, can also pass 'increasing' or 'decreasing' to change sort direction}
\item{assay}{Name of assay to use, defaults to the active assay}
\item{group.by}{Group (color) cells in different ways (for example, orig.ident)}
\item{split.by}{A factor in object metadata to split the plot by, pass 'ident'
to split by cell identity'}
\item{adjust}{Adjust parameter for geom_violin}
\item{y.max}{Maximum y axis value}
\item{same.y.lims}{Set all the y-axis limits to the same values}
\item{log}{plot the feature axis on log scale}
\item{ncol}{Number of columns if multiple plots are displayed}
\item{slot}{Slot to pull expression data from (e.g. "counts" or "data")}
\item{layer}{Layer to pull expression data from (e.g. "counts" or "data")}
\item{split.plot}{plot each group of the split violin plots by multiple or
single violin shapes.}
\item{stack}{Horizontally stack plots for each feature}
\item{combine}{Combine plots into a single \code{\link[patchwork]{patchwork}ed}
ggplot object. If \code{FALSE}, return a list of ggplot}
\item{fill.by}{Color violins/ridges based on either 'feature' or 'ident'}
\item{flip}{flip plot orientation (identities on x-axis)}
\item{add.noise}{determine if adding a small noise for plotting}
\item{raster}{Convert points to raster format. Requires 'ggrastr' to be installed.}
}
\value{
A \code{\link[patchwork]{patchwork}ed} ggplot object if
\code{combine = TRUE}; otherwise, a list of ggplot objects
}
\description{
Draws a violin plot of single cell data (gene expression, metrics, PC
scores, etc.)
}
\examples{
data("pbmc_small")
VlnPlot(object = pbmc_small, features = 'PC_1')
VlnPlot(object = pbmc_small, features = 'LYZ', split.by = 'groups')
}
\seealso{
\code{\link{FetchData}}
}
\concept{visualization}