subsetGiotto: subsetGiotto

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

subsetGiotto

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 = FALSE,
  toplevel_params = 2
)

Arguments

gobject	giotto object
spat_unit	spatial unit (e.g. "cell")
feat_type	feature type (e.g. "rna", "dna", "protein")
cell_ids	cell IDs to keep
feat_ids	feature IDs to keep
gene_ids	deprecated. Use feat_ids
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

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.