Plot grid from metadata.

Usage

plotGrid(
  spe,
  reverseY = FALSE,
  group.by = NULL,
  feature = NULL,
  assay = "counts",
  type = c("raw", "log", "cpm", "logcpm"),
  cols = NULL,
  pol.border = FALSE,
  pol.alpha = 1,
  probs = 0,
  label = NULL
)

Arguments

spe: A SpatialExperiment object.
reverseY: Reverse y coordinates.
group.by: values to group polygons by. Must be in spe@metadata$grid_density, or colData(spe) if gridLevelAnalysis is TRUE. 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.
pol.border: Boolean. Whether to draw border for each polygon.
pol.alpha: alpha of points between 0 and 1.
probs: Numeric value between 0 and 1, used for filtering uninformative grid. Only applicable for continuous values.
label: label for the legend

Value

A ggplot object.

Examples


data("xenium_bc_spe")

spe <- gridDensity(spe)

plotGrid(spe, group.by = "x_grid")