swh:1:snp:0da231f3ffdb3226650880f1b61d5d5cdcbd749b
Tip revision: 656fc8b562d53e5d0cedda9e09d9dda81e8c00e9 authored by David Collins on 29 February 2024, 13:44:33 UTC
Merge pull request #8550 from satijalab/develop
Merge pull request #8550 from satijalab/develop
Tip revision: 656fc8b
SpatialPlot.Rd
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/visualization.R, R/convenience.R
\name{SpatialPlot}
\alias{SpatialPlot}
\alias{SpatialDimPlot}
\alias{SpatialFeaturePlot}
\title{Visualize spatial clustering and expression data.}
\usage{
SpatialPlot(
object,
group.by = NULL,
features = NULL,
images = NULL,
cols = NULL,
image.alpha = 1,
crop = TRUE,
slot = "data",
keep.scale = "feature",
min.cutoff = NA,
max.cutoff = NA,
cells.highlight = NULL,
cols.highlight = c("#DE2D26", "grey50"),
facet.highlight = FALSE,
label = FALSE,
label.size = 5,
label.color = "white",
label.box = TRUE,
repel = FALSE,
ncol = NULL,
combine = TRUE,
pt.size.factor = 1.6,
alpha = c(1, 1),
stroke = 0.25,
interactive = FALSE,
do.identify = FALSE,
identify.ident = NULL,
do.hover = FALSE,
information = NULL
)
SpatialDimPlot(
object,
group.by = NULL,
images = NULL,
cols = NULL,
crop = TRUE,
cells.highlight = NULL,
cols.highlight = c("#DE2D26", "grey50"),
facet.highlight = FALSE,
label = FALSE,
label.size = 7,
label.color = "white",
repel = FALSE,
ncol = NULL,
combine = TRUE,
pt.size.factor = 1.6,
alpha = c(1, 1),
image.alpha = 1,
stroke = 0.25,
label.box = TRUE,
interactive = FALSE,
information = NULL
)
SpatialFeaturePlot(
object,
features,
images = NULL,
crop = TRUE,
slot = "data",
keep.scale = "feature",
min.cutoff = NA,
max.cutoff = NA,
ncol = NULL,
combine = TRUE,
pt.size.factor = 1.6,
alpha = c(1, 1),
image.alpha = 1,
stroke = 0.25,
interactive = FALSE,
information = NULL
)
}
\arguments{
\item{object}{A Seurat object}
\item{group.by}{Name of meta.data column to group the data by}
\item{features}{Name of the feature to visualize. Provide either group.by OR
features, not both.}
\item{images}{Name of the images to use in the plot(s)}
\item{cols}{Vector of colors, each color corresponds to an identity class.
This may also be a single character or numeric value corresponding to a
palette as specified by \code{\link[RColorBrewer]{brewer.pal.info}}. By
default, ggplot2 assigns colors}
\item{image.alpha}{Adjust the opacity of the background images. Set to 0 to
remove.}
\item{crop}{Crop the plot in to focus on points plotted. Set to \code{FALSE} to show
entire background image.}
\item{slot}{If plotting a feature, which data slot to pull from (counts,
data, or scale.data)}
\item{keep.scale}{How to handle the color scale across multiple plots. Options are:
\itemize{
\item \dQuote{feature} (default; by row/feature scaling): The plots for
each individual feature are scaled to the maximum expression of the
feature across the conditions provided to \code{split.by}
\item \dQuote{all} (universal scaling): The plots for all features and
conditions are scaled to the maximum expression value for the feature
with the highest overall expression
\item \code{NULL} (no scaling): Each individual plot is scaled to the
maximum expression value of the feature in the condition provided to
\code{split.by}; be aware setting \code{NULL} will result in color
scales that are not comparable between plots
}}
\item{min.cutoff, max.cutoff}{Vector of minimum and maximum cutoff
values for each feature, may specify quantile in the form of 'q##' where '##'
is the quantile (eg, 'q1', 'q10')}
\item{cells.highlight}{A list of character or numeric vectors of cells to
highlight. If only one group of cells desired, can simply pass a vector
instead of a list. If set, colors selected cells to the color(s) in
cols.highlight}
\item{cols.highlight}{A vector of colors to highlight the cells as; ordered
the same as the groups in cells.highlight; last color corresponds to
unselected cells.}
\item{facet.highlight}{When highlighting certain groups of cells, split each
group into its own plot}
\item{label}{Whether to label the clusters}
\item{label.size}{Sets the size of the labels}
\item{label.color}{Sets the color of the label text}
\item{label.box}{Whether to put a box around the label text (geom_text vs
geom_label)}
\item{repel}{Repels the labels to prevent overlap}
\item{ncol}{Number of columns if plotting multiple plots}
\item{combine}{Combine plots into a single gg object; note that if TRUE;
themeing will not work when plotting multiple features/groupings}
\item{pt.size.factor}{Scale the size of the spots.}
\item{alpha}{Controls opacity of spots. Provide as a vector specifying the
min and max for SpatialFeaturePlot. For SpatialDimPlot, provide a single
alpha value for each plot.}
\item{stroke}{Control the width of the border around the spots}
\item{interactive}{Launch an interactive SpatialDimPlot or SpatialFeaturePlot
session, see \code{\link{ISpatialDimPlot}} or
\code{\link{ISpatialFeaturePlot}} for more details}
\item{do.identify, do.hover}{DEPRECATED in favor of \code{interactive}}
\item{identify.ident}{DEPRECATED}
\item{information}{An optional dataframe or matrix of extra information to be displayed on hover}
}
\value{
If \code{do.identify}, either a vector of cells selected or the object
with selected cells set to the value of \code{identify.ident} (if set). Else,
if \code{do.hover}, a plotly object with interactive graphics. Else, a ggplot
object
}
\description{
SpatialPlot plots a feature or discrete grouping (e.g. cluster assignments) as
spots over the image that was collected. We also provide SpatialFeaturePlot
and SpatialDimPlot as wrapper functions around SpatialPlot for a consistent
naming framework.
}
\examples{
\dontrun{
# For functionality analagous to FeaturePlot
SpatialPlot(seurat.object, features = "MS4A1")
SpatialFeaturePlot(seurat.object, features = "MS4A1")
# For functionality analagous to DimPlot
SpatialPlot(seurat.object, group.by = "clusters")
SpatialDimPlot(seurat.object, group.by = "clusters")
}
}
\concept{convenience}
\concept{spatial}
\concept{visualization}