Create a new boundaries assay with buffers

This function takes in an existing MoleculeExperiment object and generates a new boundaries assay with added buffers. This can be useful for visualisation and for countMolecules.

Usage

bufferBoundaries(me, assayName = "cell", ...)

Arguments

me

A MoleculeExperiment object.

assayName

Character string (default "cell") specifying the existing boundaries assay that should have buffer added.

...

Arguments that pass to internal functions. The most relevant parameter is buffer (default 0).

Value

A boundaries assay with essential columns and vertices with added buffer.

Examples

repoDir <- system.file("extdata", package = "MoleculeExperiment")
repoDir <- paste0(repoDir, "/xenium_V1_FF_Mouse_Brain")
me <- readXenium(repoDir,
  keepCols = "essential"
)
MoleculeExperiment::boundaries(me, "cell_buffer") <- bufferBoundaries(
  me,
  assayName = "cell", buffer = 1
)

library(ggplot2)
ggplot_me() +
  geom_polygon_me(me, assayName = "cell", fill = "grey") +
  geom_polygon_me(me, assayName = "cell_buffer", fill = NA, colour = "red") +
  geom_point_me(me) +
  coord_cartesian(
    xlim = c(4900, 4919.98),
    ylim = c(6400.02, 6420)
  )