Plot spatial probability map for a cell type — plot_probability

Draws a spatial scatter plot colored by soft-gating probability for a given cell type (e.g., "T cell", "Tumor").

Usage

plot_probability_map(
  spe,
  cell_type,
  image_col = "imageID",
  image_index = NULL,
  x_col = NULL,
  y_col = NULL,
  point_size = 0.8
)

Arguments

spe: SpatialExperiment / SingleCellExperiment with P_* columns in colData.
cell_type: Character. Must match the lineage_table$cell_type used in run_soft_gating().
image_col: Column name for image ID (default "imageID").
image_index: Numeric indices or character IDs of images to plot. Defaults to all images. If length > 1, results are faceted by image.
x_col: Coordinate column names (default auto-detect).
y_col: Coordinate column names (default auto-detect).
point_size: Size of points.

Value

A ggplot object.

Examples

data("cytoGateR_example", package = "cytoGateR")
spe <- cytoGateR_example
plot_probability_map(
  spe,
  cell_type = "Tumor",
  image_col = "image_name",
  image_index = 1
)