subsetGiotto

Subsets Giotto object including previous analyses. For subsetting the subcellular information only without editing the aggregate information, use subsetGiottoLocsSubcellular

Usage

subsetGiotto(
  gobject,
  spat_unit = ":all:",
  feat_type = "rna",
  cell_ids = NULL,
  feat_ids = NULL,
  poly_info = NULL,
  all_spat_units = NULL,
  all_feat_types = NULL,
  spat_unit_fsub = ":all:",
  feat_type_ssub = ":all:",
  verbose = FALSE,
  toplevel_params = 2
)

Arguments

gobject

giotto object

spat_unit, feat_type

character vector. (default = ':all:') One or more spatial units or feature types to subset. Accepts ':all:' as a token to subset across all available.

cell_ids

character. cell IDs to keep

feat_ids

character. feature IDs to keep

poly_info

character. polygon info(s) to subset if present. (defaults to be the same as the spat_unit)

all_spat_units

deprecated. use spat_unit_fsub = ':all:'

all_feat_types

deprecated. use feat_type_ssub = ':all:'

spat_unit_fsub

character vector. (default = ':all:') limit feat_id subsets to these spat_units

feat_type_ssub

character vector. (default = ':all:') limit cell_id subsets to these feat_types

verbose

be verbose

toplevel_params

parameters to extract

Value

giotto object

Details

Subsets a Giotto object for a specific spatial unit and feature type