Plot cells based on spatial coordinates.

Usage

plotSpatial(
  spe,
  group.by = NULL,
  feature = NULL,
  assay = "counts",
  type = c("raw", "log", "cpm", "logcpm"),
  cols = NULL,
  highlight = NULL,
  cols.highlight = NULL,
  pt.shape = 16,
  pt.size = 0.3,
  pt.size.highlight = 1,
  pt.alpha = 0.5,
  label = NULL,
  cols.scale = NULL,
  reverseY = NULL,
  ...
)

Arguments

spe: A SpatialExperiment object.
group.by: values to group points by. Must be in colData of spe. If NULL, will try with 'cols' if available.
feature: Feature to group polygons by. Must be in rownames(spe).
assay: Name of assay to use for plotting feature.
type: Transformation to apply for the group/feature. Options are "raw" , "log", "cpm", "logcpm", or a function that accepts and returns a vector of the same length.
cols: Colour palette. Can be a vector of colours or a function that accepts an integer n and return n colours.
highlight: Optional cells to emphasise, given as either a vector of group.by levels (characters or cluster numbers), or a logical vector of length ncol(spe) selecting cells directly. Highlighted cells are drawn last (on top) at pt.size.highlight; all other cells are light grey at pt.size.
cols.highlight: Colour(s) for the highlighted cells. Defaults to NULL, which keeps each level's usual group.by palette colour. A single colour (e.g. "red") colours all highlighted cells the same; a vector matching the number of 'highlight' entries gives one colour per level (matched by position).
pt.shape: shape of points.
pt.size: size of points.
pt.size.highlight: size of highlighted points (see highlight).
pt.alpha: alpha of points between 0 and 1.
label: label for the legend
cols.scale: vector of position for color if colors should not be evenly positioned. See scale_color_gradientn. Only applicable for continuous values.
reverseY: Logical. Whether to reverse Y coordinates. Default is TRUE if the spe contains an image (even if not plotted) and FALSE if otherwise.
...: Parameters pass to plotImage

Value

A ggplot object.

Examples


data("xenium_bc_spe")

plotSpatial(spe, group.by = "cell_type", pt.size = 0.5, pt.alpha = 0.6)