Plot cells based on spatial coordinates.

Plot cells based on spatial coordinates.

Usage

plotSpatial(
  spe,
  reverseY = FALSE,
  group.by = NULL,
  feature = NULL,
  assay = "counts",
  type = c("raw", "log", "cpm", "logcpm"),
  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.

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.

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)