showGiottoSpatLocs

shows the available spatial locations

Usage

showGiottoSpatLocs(gobject, nrows = 4)

Arguments

gobject

giotto object

nrows

number of rows to print for each spatial location data.table

Value

prints the name and small subset of available data.table

See also

Other functions to show data in giotto object: showGiottoCellMetadata(), showGiottoDimRed(), showGiottoExpression(), showGiottoFeatInfo(), showGiottoFeatMetadata(), showGiottoImageNames(), showGiottoNearestNetworks(), showGiottoSpatEnrichments(), showGiottoSpatGrids(), showGiottoSpatNetworks(), showGiottoSpatialInfo()

Examples

g <- GiottoData::loadGiottoMini("visium")
#> 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"

showGiottoSpatLocs(g)
#> └──Spatial unit "cell"
#>    └──S4 spatLocsObj "raw" coordinates:   (624 rows)
#>          An object of class spatLocsObj 
#>          provenance: cell
#>              ------------------------
#>             sdimx sdimy            cell_ID
#>             <int> <int>             <char>
#>          1:  5477 -4125 AAAGGGATGTAGCAAG-1
#>          2:  5959 -2808 AAATGGCATGTCTTGT-1
#>          3:  4720 -5202 AAATGGTCAATGTGCC-1
#>          4:  5202 -5322 AAATTAACGGGTAGCT-1
#>          
#>          ranges:
#>               sdimx sdimy
#>          [1,]  3069 -5442
#>          [2,]  6441 -2568
#>          
#>          
#>