showGiottoDimRed

shows the available dimension reductions

Usage

showGiottoDimRed(gobject, nrows = 3, ncols = 2)

Arguments

gobject

giotto object

nrows

number of coordinates rows to print

ncols

number of coordinates columns to print

Value

prints the name and small subset of available dimension reduction coordinates

See also

Other functions to show data in giotto object: showGiottoCellMetadata(), showGiottoExpression(), showGiottoFeatInfo(), showGiottoFeatMetadata(), showGiottoImageNames(), showGiottoNearestNetworks(), 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"

showGiottoDimRed(g)
#> Dim reduction on cells:
#>  ------------------------- 
#> 
#> .
#> └──Spatial unit "cell"
#>    └──Feature type "rna"
#>       ├──Dim reduction type "pca"
#>       │  ├──S4 dimObj "pca" coordinates:   (624 rows 100 cols)
#>       │  │                            Dim.1      Dim.2
#>       │  │     AAAGGGATGTAGCAAG-1  0.801127   2.874369
#>       │  │     AAATGGCATGTCTTGT-1  6.995542  -2.010611
#>       │  │     AAATGGTCAATGTGCC-1 -7.813633 -12.305266
#>       │  │  
#>       │  └──S4 dimObj "custom_pca" coordinates:   (624 rows 100 cols)
#>       │                                Dim.1     Dim.2
#>       │        AAAGGGATGTAGCAAG-1 -0.4547083  3.383001
#>       │        AAATGGCATGTCTTGT-1 -6.2679882  1.503456
#>       │        AAATGGTCAATGTGCC-1 10.2690789 -7.006071
#>       │     
#>       ├──Dim reduction type "umap"
#>       │  ├──S4 dimObj "umap" coordinates:   (624 rows 2 cols)
#>       │  │                             Dim.1      Dim.2
#>       │  │     AAAGGGATGTAGCAAG-1  -3.975629   4.401250
#>       │  │     AAATGGCATGTCTTGT-1 -16.788569 -20.950487
#>       │  │     AAATGGTCAATGTGCC-1  27.206731  -9.034316
#>       │  │  
#>       │  └──S4 dimObj "custom_umap" coordinates:   (624 rows 2 cols)
#>       │                                Dim.1      Dim.2
#>       │        AAAGGGATGTAGCAAG-1  -3.731145  -3.665592
#>       │        AAATGGCATGTCTTGT-1 -14.201382 -23.566582
#>       │        AAATGGTCAATGTGCC-1  29.736043   6.478635
#>       │     
#>       └──Dim reduction type "tsne"
#>          └──S4 dimObj "tsne" coordinates:   (624 rows 2 cols)
#>                                        Dim.1      Dim.2
#>                AAAGGGATGTAGCAAG-1 -3.4389554  -1.690378
#>                AAATGGCATGTCTTGT-1  0.4290782 -18.060330
#>                AAATGGTCAATGTGCC-1 17.8533998  12.975694
#>