SingleSpatialPlot: Base plotting function for all Spatial plots

Description

Base plotting function for all Spatial plots

Usage

SingleSpatialPlot(
  data,
  image,
  cols = NULL,
  image.alpha = 1,
  pt.alpha = NULL,
  crop = TRUE,
  pt.size.factor = NULL,
  stroke = 0.25,
  col.by = NULL,
  alpha.by = NULL,
  cells.highlight = NULL,
  cols.highlight = c("#DE2D26", "grey50"),
  geom = c("spatial", "interactive", "poly"),
  na.value = "grey50"
)

Value

A ggplot2 object

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.
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
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