Aggregate Spatial Features Covered by Polygon Geometries

Aggregate features (either feat_info OR image_names) with polygons (spat_info). Under the hood, this is performed in two steps:

Find the overlapped features via the lower-level generic calculateOverlap()
Summarize the overlapped features as a matrix via overlapToMatrix()

Usage

aggregateFeatures(
  gobject,
  spat_info = NULL,
  feat_info = NULL,
  image_names = NULL,
  new_spat_unit = NULL,
  new_feat_type = NULL,
  name = "raw",
  poly_subset_ids = NULL,
  feat_subset_column = NULL,
  feat_subset_values = NULL,
  feat_count_column = NULL,
  fun = "sum",
  return_gobject = TRUE,
  verbose = TRUE,
  ...
)

Arguments

gobject: giotto object containing spatial data to aggregate.
spat_info: character. Name of polygon information to use to aggregate features with.
feat_info: character. Name of feature point detections to be aggregated.
image_names: character. Name of image(s) containing intensity values to be aggregated.
new_spat_unit: character (optional). Name of spatial unit to assign the expression info to. Default is the same as spat_info.
new_feat_type: character (optional). Name of feature type to assign the expression info to. Default is the same as feat_info when used. When image_names is used instead, default is "protein".
name: character. (default = "raw") Name to assign the output expresssion values information.
poly_subset_ids: character vector. (optional) Specific poly_IDs to use
feat_subset_column: character. (optional) feature info attribute to subset feature points on when performing overlap calculation.
feat_subset_values: (optional) values matched against in feat_subset_column in order to subset feature points when performing overlap calculation.
feat_count_column: character. (optional) feature info column with counts information. Useful in cases when more than one detection is reported per point.
fun: character (default = "sum"). A function usable by exactextractr::exact_extract() to aggregate image intensity values.
return_gobject: logical (default = TRUE). Whether to return the giotto object or just the aggregated expression values as exprObj class.
verbose: logical. Whether to be verbose.
...: Additional params to pass to the overlap calculation method. None implemented for point overlaps. For intensity overlaps, passes to exactextractr::exact_extract() and additionally the function requested with the fun param.

Value

giotto when return_gobject=TRUE, exprObj when return_gobject=FALSE

Details

feat_subset_column, feat_subset_values, and feat_count_column are specific to overlaps on feature points info, and should not be provided when overlapping image data.