show the available giotto spatial polygon information
See also
Other functions to show data in giotto object:
showGiottoCellMetadata(),
showGiottoDimRed(),
showGiottoExpression(),
showGiottoFeatInfo(),
showGiottoFeatMetadata(),
showGiottoImageNames(),
showGiottoNearestNetworks(),
showGiottoSpatEnrichments(),
showGiottoSpatGrids(),
showGiottoSpatLocs(),
showGiottoSpatNetworks()
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"
showGiottoSpatialInfo(g)
#> For Spatial info: z0
#>
#> An object of class giottoPolygon
#> spat_unit : "z0"
#> Spatial Information:
#> 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
#> centroids : calculated
#> overlaps : rna
#> -----------------------------
#>
#> For Spatial info: z1
#>
#> An object of class giottoPolygon
#> spat_unit : "z1"
#> Spatial Information:
#> class : SpatVector
#> geometry : polygons
#> dimensions : 504, 1 (geometries, attributes)
#> extent : 6391.466, 6903.573, -5153.897, -4694.873 (xmin, xmax, ymin, ymax)
#> source : z1_spatInfo_spatVector.shp
#> coord. ref. :
#> names : poly_ID
#> type : <chr>
#> values : 40951783403982682273285375368232495429
#> 17685062374745280598492217386845129350
#> 223553142498364321238189328942498473503
#> centroids : calculated
#> overlaps : rna
#> -----------------------------
#>
#> For Spatial info: aggregate
#>
#> An object of class giottoPolygon
#> spat_unit : "aggregate"
#> Spatial Information:
#> class : SpatVector
#> geometry : polygons
#> dimensions : 462, 4 (geometries, attributes)
#> extent : 6391.466, 6903.573, -5153.897, -4694.868 (xmin, xmax, ymin, ymax)
#> source : aggregate_spatInfo_spatVector.shp
#> coord. ref. :
#> names : poly_ID stack agg_n valid
#> type : <chr> <chr> <int> <int>
#> values : 100210519278873141813371~ NA 2 1
#> 101161259912191124732236~ NA 2 1
#> 101488859781016188084173~ NA 2 1
#> centroids : calculated
#> overlaps : rna
#> -----------------------------
#>