shows the available feature metadata
See also
Other functions to show data in giotto object:
showGiottoCellMetadata(),
showGiottoDimRed(),
showGiottoExpression(),
showGiottoFeatInfo(),
showGiottoImageNames(),
showGiottoNearestNetworks(),
showGiottoSpatEnrichments(),
showGiottoSpatGrids(),
showGiottoSpatLocs(),
showGiottoSpatNetworks(),
showGiottoSpatialInfo()
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"
showGiottoFeatMetadata(g)
#> ├──Spatial unit "z0"
#> │ └──Feature type "rna"
#> │ An object of class featMetaObj
#> │ spat_unit : "z0"
#> │ feat_type : "rna"
#> │ provenance: z0
#> │
#> │ feat_ID
#> │ <char>
#> │ 1: Mlc1
#> │ 2: Gprc5b
#> │ 3: Gfap
#> │
#> ├──Spatial unit "z1"
#> │ └──Feature type "rna"
#> │ An object of class featMetaObj
#> │ spat_unit : "z1"
#> │ feat_type : "rna"
#> │ provenance: z1
#> │
#> │ feat_ID
#> │ <char>
#> │ 1: Mlc1
#> │ 2: Gprc5b
#> │ 3: Gfap
#> │
#> └──Spatial unit "aggregate"
#> └──Feature type "rna"
#> An object of class featMetaObj
#> spat_unit : "aggregate"
#> feat_type : "rna"
#> provenance: z0 z1
#>
#> feat_ID nr_cells perc_cells total_expr mean_expr mean_expr_det hvg_orig
#> <char> <int> <num> <num> <num> <num> <char>
#> 1: Mlc1 80 17.31602 526.5915 1.139808 6.582394 no
#> 2: Gprc5b 138 29.87013 944.0153 2.043323 6.840690 no
#> 3: Gfap 151 32.68398 1229.1943 2.660594 8.140359 yes
#> var hvf
#> <num> <char>
#> 1: 1.815718 yes
#> 2: 2.388911 yes
#> 3: 12.899599 yes
#>