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calculateOverlapRaster

Source: R/aggregate.R
calculateOverlapRaster.Rd

calculate overlap between cellular structures (polygons) and features (points).

Usage

calculateOverlapRaster(
  gobject,
  name_overlap = NULL,
  spatial_info = NULL,
  poly_ID_names = NULL,
  feat_info = NULL,
  feat_subset_column = NULL,
  feat_subset_values = NULL,
  feat_count_column = NULL,
  return_gobject = TRUE,
  verbose = TRUE,
  feat_subset_ids = deprecated(),
  count_info_column = deprecated()
)

Arguments

gobject

giotto object

name_overlap

name for the overlap results (default to feat_info parameter)

spatial_info

character. name polygon information

poly_ID_names

(optional) list of poly_IDs to use

feat_info

character. name of feature information

feat_subset_column

feature info column to subset features with

feat_subset_values

value(s) within feature info feat_subset_column to use for subsetting

feat_count_column

column with count information (optional)

return_gobject

return giotto object (default: TRUE)

verbose

be verbose

feat_subset_ids

deprecated. Use feat_subset_values instead.

count_info_column

deprecated. Use feat_count_column instead.

Value

giotto object or spatVector with overlapping information

Details

Serial overlapping function.

See also

.calculate_overlap_raster()

Examples

g <- GiottoData::loadGiottoMini("vizgen")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 4. read Giotto image information
#> python already initialized in this session
#>  active environment : 'giotto_env'
#>  python version : 3.10

calculateOverlapRaster(g)
#> Warning: `calculateOverlapRaster()` was deprecated in GiottoClass 0.4.7.
#> ℹ Please use `aggregateFeatures()` instead.
#> ℹ `calculateOverlap()` is another option if only the overlap step is desired.
#> 1. convert polygon to raster
#> 2. overlap raster and points
#> An object of class giotto 
#> >Active spat_unit:  z0 
#> >Active feat_type:  rna 
#> dimensions    : 337, 498 (features, cells)
#> [SUBCELLULAR INFO]
#> polygons      : z0 z1 aggregate 
#> features      : rna 
#> [AGGREGATE INFO]
#> expression -----------------------
#>   [z0][rna] raw
#>   [z1][rna] raw
#>   [aggregate][rna] raw normalized scaled pearson
#> spatial locations ----------------
#>   [z0] raw
#>   [z1] raw
#>   [aggregate] raw
#> spatial networks -----------------
#>   [aggregate] Delaunay_network kNN_network
#> spatial enrichments --------------
#>   [aggregate][rna] cluster_metagene
#> dim reduction --------------------
#>   [aggregate][rna] pca umap tsne
#> nearest neighbor networks --------
#>   [aggregate][rna] sNN.pca
#> attached images ------------------
#> images      : 4 items...
#> 
#> 
#> Use objHistory() to see steps and params used