calculateOverlapParallel#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/giotto_structures.R#L2218

Description#

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

Usage#

calculateOverlapParallel(
  gobject,
  name_overlap = NULL,
  spatial_info = "cell",
  feat_info = "rna",
  poly_ID_names = "all",
  polygon_group_size = 500,
  return_gobject = TRUE,
  verbose = TRUE
)

Arguments#

Argument

Description

gobject

giotto object

name_overlap

name for the overlap results (default to feat_info parameter)

spatial_info

polygon information

feat_info

feature information

poly_ID_names

list of poly_IDs to use

polygon_group_size

number of polygons to process per parallelization group

return_gobject

return giotto object (default: TRUE)

verbose

be verbose

Details#

parallel follows the future approach. This means that plan(multisession) does not work, since the underlying terra objects are internal C pointers. plan(multicore) is also not supported for Rstudio users.

Value#

giotto object or spatVector with overlapping information