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 = spat_unit,
  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

Examples

g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#>  active environment : 'giotto_env'
#>  python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/share/miniconda/envs/giotto_env/bin/python"

subsetGiotto(g, cell_ids = c("AACTCGATGGCGCAGT-1", "GGCTGGCTAGCTTAAA-1"))
#> An object of class giotto 
#> >Active spat_unit:  cell 
#> >Active feat_type:  rna 
#> dimensions    : 634, 2 (features, cells)
#> [SUBCELLULAR INFO]
#> polygons      : cell 
#> [AGGREGATE INFO]
#> expression -----------------------
#>   [cell][rna] raw normalized scaled
#> spatial locations ----------------
#>   [cell] raw
#> spatial networks -----------------
#>   [cell] Delaunay_network spatial_network
#> spatial enrichments --------------
#>   [cell][rna] cluster_metagene DWLS
#> dim reduction --------------------
#>   [cell][rna] pca custom_pca umap custom_umap tsne
#> nearest neighbor networks --------
#>   [cell][rna] sNN.pca custom_NN
#> attached images ------------------
#> images      : alignment image 
#> 
#> 
#> Use objHistory() to see steps and params used