SpatialPlot: Visualize spatial clustering and expression data.

In satijalab/seurat: Tools for Single Cell Genomics

Visualize spatial clustering and expression data.

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.

Usage

SpatialPlot(
  object,
  group.by = NULL,
  features = NULL,
  images = NULL,
  cols = NULL,
  image.alpha = 1,
  image.scale = "lowres",
  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),
  shape = 21,
  stroke = NA,
  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,
  image.scale = "lowres",
  shape = 21,
  stroke = NA,
  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,
  image.scale = "lowres",
  shape = 21,
  stroke = NA,
  interactive = FALSE,
  information = NULL
)

Arguments

object	A Seurat object
group.by	Name of meta.data column to group the data by
features	Name of the feature to visualize. Provide either group.by OR features, not both.
images	Name of the images to use in the plot(s)
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 brewer.pal.info. By default, ggplot2 assigns colors
image.alpha	Adjust the opacity of the background images. Set to 0 to remove.
image.scale	Choose the scale factor ("lowres"/"hires") to apply in order to matchthe plot with the specified 'image' - defaults to "lowres"
crop	Crop the plot in to focus on points plotted. Set to FALSE to show entire background image.
slot	If plotting a feature, which data slot to pull from (counts, data, or scale.data)
keep.scale	How to handle the color scale across multiple plots. Options are: “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 split.by “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 NULL (no scaling): Each individual plot is scaled to the maximum expression value of the feature in the condition provided to split.by; be aware setting NULL will result in color scales that are not comparable between plots
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')
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
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.
facet.highlight	When highlighting certain groups of cells, split each group into its own plot
label	Whether to label the clusters
label.size	Sets the size of the labels
label.color	Sets the color of the label text
label.box	Whether to put a box around the label text (geom_text vs geom_label)
repel	Repels the labels to prevent overlap
ncol	Number of columns if plotting multiple plots
combine	Combine plots into a single gg object; note that if TRUE; themeing will not work when plotting multiple features/groupings
pt.size.factor	Scale the size of the spots.
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.
shape	Control the shape of the spots - same as the ggplot2 parameter. The default is 21, which plots circles - use 22 to plot squares.
stroke	Control the width of the border around the spots
interactive	Launch an interactive SpatialDimPlot or SpatialFeaturePlot session, see ISpatialDimPlot or ISpatialFeaturePlot for more details
do.identify, do.hover	DEPRECATED in favor of interactive
identify.ident	DEPRECATED
information	An optional dataframe or matrix of extra information to be displayed on hover

Value

If do.identify, either a vector of cells selected or the object with selected cells set to the value of identify.ident (if set). Else, if do.hover, a plotly object with interactive graphics. Else, a ggplot object

Examples

## Not run: 
# 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")

## End(Not run)

satijalab/seurat documentation built on May 11, 2024, 4:04 a.m.