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Plot ROIs on spatial.

Source: R/plotROI.R
plotROI.Rd

Plot ROIs on spatial.

Usage

plotROI(
  spe,
  roi = NULL,
  id = "cell_type",
  label = TRUE,
  show.legend = FALSE,
  ...
)

Arguments

spe

A SpatialExperiment object.

roi

Character. The name of the group or cell type on which the roi is computed. All cell types are chosen if NULL or 'overall'.

id

Character. The name of the column of colData(spe) containing the cell type identifiers. Set to cell_type by default.

label

Logical. Show ROI label or not.

show.legend

Logical. Show legend or not.

...

Aesthetic mappings pass for point.

Value

A ggplot object.

Examples


data("xenium_bc_spe")

coi <- c("Breast cancer", "Fibroblasts")

spe <- gridDensity(spe, coi = coi)

spe <- findROI(spe, coi = coi, method = "walktrap", steps = 5)

plotROI(spe, roi = coi, pt.size = 0.3, pt.alpha = 0.2)