Subset by spatial locations

Subsets Giotto object spatially by defining a set of cropping bounds. The information to be subset is preferred to be from spatial locations. If no spat_loc_name is given, the first available set of spatial locations for the spat_unit will be picked. If no spatial locations are available, the polygon information will be subset. Spatial IDs surviving the crop are then applied to the rest of the Giotto object using subsetGiotto.

Usage

subsetGiottoLocs(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  feat_type_ssub = ":all:",
  spat_loc_name = NULL,
  x_max = NULL,
  x_min = NULL,
  y_max = NULL,
  y_min = NULL,
  z_max = NULL,
  z_min = NULL,
  poly_info = NULL,
  return_gobject = TRUE,
  verbose = FALSE,
  toplevel_params = 5
)

Arguments

gobject

giotto object

spat_unit

spatial unit to subset

feat_type

(optional) feat type to use if return_gobject = TRUE and a combined data.table output is desired.

feat_type_ssub

which feat types across which to apply the spatial subset

spat_loc_name

name of spatial locations to use within spat_unit

x_max, x_min, y_max, y_min, z_max, z_min

minimum and maximum x, y, and z coordinates to subset to

poly_info

character. polygon information to subset (considered separately from the spat_units to subset)

return_gobject

return Giotto object

verbose

be verbose

toplevel_params

parameters to extract

Value

giotto object

Details

If return_gobject = FALSE, then a filtered combined metadata data.table will be returned

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"

subsetGiottoLocs(g, x_max = 4000, y_max = -1000)
#> An object of class giotto 
#> >Active spat_unit:  cell 
#> >Active feat_type:  rna 
#> dimensions    : 634, 175 (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