Plot cells based on spatial coordinates. — plotSpatial • scider

Plot cells based on spatial coordinates.

Usage

plotSpatial(
  spe,
  reverseY = FALSE,
  group.by = NULL,
  cols = NULL,
  pt.shape = 16,
  pt.size = 0.3,
  pt.alpha = 0.5
)

Arguments

spe: A SpatialExperiment object.
reverseY: Reverse y coordinates.
group.by: values to group points by. Must be in colData of spe. If NULL, will try with 'cols' if available.
cols: Colour palette. Can be a vector of colours or a function that accepts an integer n and return n colours.
pt.shape: shape of points.
pt.size: size of points.
pt.alpha: alpha of points between 0 and 1.

Value

A ggplot object.

Examples


data("xenium_bc_spe")

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