SingleSpatialPlot: Base plotting function for all Spatial plots

In satijalab/seurat: Tools for Single Cell Genomics

Base plotting function for all Spatial plots

Description

Base plotting function for all Spatial plots

Usage

SingleSpatialPlot(
  data,
  image,
  cols = NULL,
  image.alpha = 1,
  image.scale = "lowres",
  pt.alpha = NULL,
  crop = TRUE,
  pt.size.factor = NULL,
  shape = 21,
  stroke = NA,
  col.by = NULL,
  alpha.by = NULL,
  cells.highlight = NULL,
  cols.highlight = c("#DE2D26", "grey50"),
  geom = c("spatial", "interactive", "poly"),
  na.value = "grey50"
)

Arguments

data	Data.frame with info to be plotted
image	SpatialImage object to be plotted
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"
pt.alpha	Adjust the opacity of the points if plotting a SpatialDimPlot
crop	Crop the plot in to focus on points plotted. Set to FALSE to show entire background image.
pt.size.factor	Sets the size of the points relative to spot.radius
shape	Control the shape of the spots - same as the ggplot2 parameter. The default is 21, which plots cirlces - use 22 to plot squares.
stroke	Control the width of the border around the spots
col.by	Mapping variable for the point color
alpha.by	Mapping variable for the point alpha value
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.
geom	Switch between normal spatial geom and geom to enable hover functionality
na.value	Color for spots with NA values

Value

A ggplot2 object

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