shows the available matrices
See also
Other functions to show data in giotto object:
showGiottoCellMetadata(),
showGiottoDimRed(),
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"
showGiottoExpression(g)
#> └──Spatial unit "cell"
#> └──Feature type "rna"
#> ├──Expression data "raw" values:
#> │ An object of class exprObj : "raw"
#> │ spat_unit : "cell"
#> │ feat_type : "rna"
#> │ provenance: cell
#> │
#> │ contains:
#> │ 634 x 624 sparse Matrix of class "dgCMatrix"
#> │
#> │ Gna12 1 2 1 1 9 1 3 5 3 . . 10 7 ......
#> │ Ccnd2 . 1 1 . . 1 . 1 1 . . . 3 ......
#> │ Btbd17 . 1 1 1 . . 2 . . . . . . ......
#> │
#> │ ........suppressing 611 columns and 628 rows in show(); maybe adjust options(max.print=, width=)
#> │
#> │ Gm19935 . 1 . . . . . . . . 1 . . ......
#> │ 9630013A20Rik . . . . . . . . . . 1 . . ......
#> │ 2900040C04Rik 1 . . . . . . . . 1 . . . ......
#> │
#> │ First four colnames:
#> │ AAAGGGATGTAGCAAG-1 AAATGGCATGTCTTGT-1
#> │ AAATGGTCAATGTGCC-1 AAATTAACGGGTAGCT-1
#> │
#> ├──Expression data "normalized" values:
#> │ An object of class exprObj : "normalized"
#> │ spat_unit : "cell"
#> │ feat_type : "rna"
#> │ provenance: cell
#> │
#> │ contains:
#> │ 634 x 624 sparse Matrix of class "dgCMatrix"
#> │
#> │ Gna12 3.783033 3.929306 3.213481 3.625522 5.749157 2.399595 4.127923 4.693522 5.299374 . .
#> │ Ccnd2 . 3.021024 3.213481 . . 2.399595 . 2.578969 3.785883 . .
#> │ Btbd17 . 3.021024 3.213481 3.625522 . . 3.583641 . . . .
#> │
#> │ Gna12 5.683074 5.036423 ......
#> │ Ccnd2 . 3.871485 ......
#> │ Btbd17 . . ......
#> │
#> │ ........suppressing 611 columns and 628 rows in show(); maybe adjust options(max.print=, width=)
#> │
#> │ Gm19935 . 3.021024 . . . . . . . . 3.103487 . . ......
#> │ 9630013A20Rik . . . . . . . . . . 3.103487 . . ......
#> │ 2900040C04Rik 3.783033 . . . . . . . . 3.488189 . . . ......
#> │
#> │ First four colnames:
#> │ AAAGGGATGTAGCAAG-1 AAATGGCATGTCTTGT-1
#> │ AAATGGTCAATGTGCC-1 AAATTAACGGGTAGCT-1
#> │
#> └──Expression data "scaled" values:
#> An object of class exprObj
#> for spatial unit: "cell" and feature type: "rna"
#> Provenance: cell
#>
#> contains:
#> 634 x 624 dense matrix of class "dgeMatrix"
#>
#> [,1] [,2] [,3] [,4]
#> Gna12 0.3648960 0.3883749 0.02397458 0.2635371
#> Ccnd2 -0.9726302 0.5135323 0.59882469 -0.8883955
#> Btbd17 -0.6902939 1.0914525 1.12309944 1.3267401
#> Sox9 -0.8344595 -1.0154377 -0.84282003 -0.7614102
#>
#> First four colnames:
#> AAAGGGATGTAGCAAG-1 AAATGGCATGTCTTGT-1
#> AAATGGTCAATGTGCC-1 AAATTAACGGGTAGCT-1
#>