Get giotto polygon spatVector
Usage
getPolygonInfo(
gobject = NULL,
polygon_name = NULL,
polygon_overlap = NULL,
return_giottoPolygon = FALSE,
verbose = TRUE,
simplify = TRUE
)Arguments
- gobject
giotto object
- polygon_name
name of polygons. Default is "cell"
- polygon_overlap
include polygon overlap information
- return_giottoPolygon
(Defaults to FALSE) Return as giottoPolygon S4 object
- verbose
be verbose
- simplify
logical. Whether or not to take object out of a list when there is a length of 1.
See also
Other polygon info data accessor functions:
setPolygonInfo()
Other functions to get data from giotto object:
getCellMetadata(),
getDimReduction(),
getExpression(),
getFeatureInfo(),
getFeatureMetadata(),
getGiottoImage(),
getMultiomics(),
getNearestNetwork(),
getSpatialEnrichment(),
getSpatialGrid(),
getSpatialLocations(),
getSpatialNetwork(),
get_multiomics()
Examples
g <- GiottoData::loadGiottoMini("vizgen")
#> 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"
getPolygonInfo(g)
#> class : SpatVector
#> geometry : polygons
#> dimensions : 498, 1 (geometries, attributes)
#> extent : 6399.244, 6903.243, -5152.39, -4694.868 (xmin, xmax, ymin, ymax)
#> source : z0_spatInfo_spatVector.shp
#> coord. ref. :
#> names : poly_ID
#> type : <chr>
#> values : 40951783403982682273285375368232495429
#> 240649020551054330404932383065726870513
#> 274176126496863898679934791272921588227