Plot spatial cell boundaries — SpatialCellPlot • scop

Plot cell segmentation polygons from a boundary table or Seurat spatial image.

Usage

SpatialCellPlot(
  object = NULL,
  res = NULL,
  boundaries = NULL,
  cells = NULL,
  image = NULL,
  crop = TRUE,
  group.by = NULL,
  features = NULL,
  palette = NULL,
  palcolor = NULL,
  fill.alpha = 0.7,
  boundary.color = "grey30",
  boundary.linewidth = 0.1,
  theme_use = "theme_spatial",
  theme_args = list(),
  assay = NULL,
  layer = "data",
  ...,
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  legend.position = "right",
  legend.direction = "vertical",
  legend.title = NULL
)

Arguments

object: Optional `Seurat` object used to extract boundaries or values.
res: Optional result list containing a `boundaries` data frame.
boundaries: Optional boundary data frame.
cells: Optional cell or spot identifiers to retain.
image: Seurat image name. Multi-image objects require an explicit name.
crop: Whether to crop the plot to the selected boundaries.
group.by: Boundary column or Seurat metadata column used for filling.
features: Features to display. Multiple features return a patchwork.
palette, palcolor: Palette name or explicit colors. The default uses `"Paired"` for categories and sequential `"YlGnBu"` for numeric values. Named colors are matched to category names.
fill.alpha: Polygon fill opacity.
boundary.color, boundary.linewidth: Boundary appearance.
theme_use, theme_args: Theme used to style the plot. Default is `"theme_spatial"`.
assay: Assay used when `features` are fetched from `object`.
layer: Layer used when `features` are fetched from `object`.
...: Additional arguments passed to `ggplot2::geom_polygon()`.
combine: Return combined panels, or a named list when `FALSE`.
nrow, ncol, byrow: Layout controls for multiple feature panels.
legend.position, legend.direction, legend.title: Legend controls.

Value

A `ggplot`, patchwork, or named list of plots.

Details

Boundary tables require `cell_id`, `x`, and `y` columns in polygon vertex order. Seurat images must contain segmentation boundaries.

Examples

# Constructed polygons demonstrate plotting, not a segmentation algorithm.
boundaries <- data.frame(
  cell_id = rep(c("cell1", "cell2"), each = 4),
  x = c(0, 2, 2, 0, 3, 5, 5, 3), y = rep(c(0, 0, 1, 1), 2),
  cell_type = rep(c("A", "B"), each = 4)
)
SpatialCellPlot(boundaries = boundaries, group.by = "cell_type")