Manually merge ROIs

Usage

mergeROI(
  spe,
  roi = NULL,
  merge.list = NULL,
  remove.ids = NULL,
  id = "component",
  rename = 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'.
merge.list: A (named) list of vectors of ROI ids to be merged. Each vector in the list should be of length greater than or equal to 2. If no name is specified, the merged ROI will be named by concatenating ROIs being merged.
remove.ids: Optional. A vector of ROI ids to be removed.
id: Character. The name of the column in spe@metadata$roi that stores the ROIs to be merged. Default is "component".
rename: Logical. If TRUE, names of merge.list are ignored. ROIs will be given a new name. For the unmerged ROIs, their new names are not necessarily the same as those before merging.

Value

A SpatialExperiment object.

Examples


data("xenium_bc_spe")

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

spe <- gridDensity(spe, coi = coi)

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

spe <- mergeROI(spe, roi = coi, list("1-2" = 1:2))