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
- 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.
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 : '/usr/bin/python3'
#> python version : 3.12
calculateOverlapParallel(g, spatial_info = "z1")
#> Error: package 'future' is not yet installed
#>
#> To install:
#> install.packages(c("future"))