subsetGiotto#

Last Updated: Jan 29, 2024

Description#

Subsets Giotto object including previous analyses.

Usage#

subsetGiotto(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  cell_ids = NULL,
  feat_ids = NULL,
  gene_ids = NULL,
  poly_info = NULL,
  all_spat_units = TRUE,
  all_feat_types = TRUE,
  x_max = NULL,
  x_min = NULL,
  y_max = NULL,
  y_min = NULL,
  verbose = TRUE,
  toplevel_params = 2
)

Arguments#

gobject

giotto object

spat_unit

spatial unit

feat_type

feature type to use

cell_ids

cell IDs to keep

feat_ids

feature IDs to keep

poly_info

polygon information to use

all_spat_units

subset all spatial units with selected feature ids

all_feat_types

subset all feature type data with selected cell ids

x_max, x_min, y_max, y_min

minimum and maximum x and y coordinates to keep for feature coordinates

verbose

be verbose

toplevel_params

parameters to extract

Details#

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

Value#

giotto object