shows the available nearest neighbor networks
See also
Other functions to show data in giotto object:
showGiottoCellMetadata(),
showGiottoDimRed(),
showGiottoExpression(),
showGiottoFeatInfo(),
showGiottoFeatMetadata(),
showGiottoImageNames(),
showGiottoSpatEnrichments(),
showGiottoSpatGrids(),
showGiottoSpatLocs(),
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"
showGiottoNearestNetworks(g)
#> └──Spatial unit "cell"
#> └──Feature type "rna"
#> └──NN network type "sNN"
#> ├──S4 nnNetObj "sNN.pca" (3748 rows)
#> │ from to weight distance shared rank
#> │ <char> <char> <num> <num> <int> <int>
#> │ 1: AAAGGGATGTAGCAAG-1 CAGTGTCCGCAGAATG-1 0.3777898 1.646975 9 1
#> │ 2: AAAGGGATGTAGCAAG-1 ACGTAGATTGCTGATG-1 0.2318818 3.312541 6 2
#> │ 3: AAAGGGATGTAGCAAG-1 CGTACCTGATAGGCCT-1 0.3122768 2.202287 6 3
#> │
#> └──S4 nnNetObj "custom_NN" (1872 rows)
#> from to weight distance shared rank
#> <char> <char> <num> <num> <int> <int>
#> 1: AAAGGGATGTAGCAAG-1 AACTGGGTCCCGACGT-1 0.1492788 5.698874 2 1
#> 2: AAAGGGATGTAGCAAG-1 CAGCTCGTGCTTGTGT-1 0.1507539 5.633328 1 2
#> 3: AAAGGGATGTAGCAAG-1 CGTACCTGATAGGCCT-1 0.1566434 5.383926 1 3
#>