Get multiomics integration results

Get a multiomics integration result from a Giotto object

Usage

getMultiomics(
  gobject = NULL,
  spat_unit = NULL,
  feat_type = NULL,
  integration_method = "WNN",
  result_name = "theta_weighted_matrix"
)

Arguments

gobject

A Giotto object

spat_unit

spatial unit (e.g. 'cell')

feat_type

integrated feature type (e.g. 'rna_protein')

integration_method

multiomics integration method used. Default = 'WNN'

result_name

Default = 'theta_weighted_matrix'

Value

A multiomics integration result (e.g. theta_weighted_matrix from WNN)

See also

Other multiomics accessor functions: get_multiomics(), setMultiomics(), set_multiomics()

Other functions to get data from giotto object: getCellMetadata(), getDimReduction(), getExpression(), getFeatureInfo(), getFeatureMetadata(), getGiottoImage(), getNearestNetwork(), getPolygonInfo(), getSpatialEnrichment(), getSpatialGrid(), getSpatialLocations(), getSpatialNetwork(), get_multiomics()

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
g <- setMultiomics(
    gobject = g, result = matrix(rnorm(100), nrow = 10),
    spat_unit = "cell", feat_type = "rna_protein"
)

getMultiomics(gobject = g, spat_unit = "cell", feat_type = "rna_protein")
#>             [,1]        [,2]       [,3]       [,4]        [,5]        [,6]
#>  [1,] -2.0749896  1.60617521  0.9768600  0.9921510  0.08658439 -0.24844333
#>  [2,]  0.1114416  0.07428736 -0.3543777 -0.4675122 -0.45354911 -0.11181289
#>  [3,] -1.1542127  1.97654017 -0.6908579 -0.2283285 -0.54641552  0.23792348
#>  [4,]  0.2110702 -0.19294146 -0.4518673 -0.2969727 -0.01955325 -1.84926159
#>  [5,] -1.1017581  1.26852030  0.2796521  0.1312269 -0.46762272  0.56145707
#>  [6,]  0.3934137  1.63651131 -0.9323407 -1.5649531 -0.16431026 -0.34883770
#>  [7,]  1.8247422 -0.73388406  0.4217614 -0.8242279  1.69912784 -0.13678616
#>  [8,]  1.2634744 -1.12411793  0.8055708  1.7339741 -1.14369864 -1.19301887
#>  [9,]  1.6833105 -0.42167997 -0.7100369 -1.6379856 -0.12154774  0.03095702
#> [10,]  0.9580530  0.47359528  0.3198127  0.4041991 -0.29105927  0.23291895
#>              [,7]       [,8]        [,9]       [,10]
#>  [1,] -1.33143153 -0.3901619  1.36949166 -1.14230898
#>  [2,] -0.46128145  1.6062025  0.01060681  1.63509398
#>  [3,]  0.08372638 -0.6096521 -0.67390639  1.36615949
#>  [4,]  0.89130758 -2.7034814 -0.22344426 -1.00090962
#>  [5,]  1.62758122  0.2903812 -0.49857582 -0.64903154
#>  [6,] -1.23260939 -0.6807358 -0.12481335 -0.08602487
#>  [7,]  0.68610440  0.3186103  0.74445644  1.29266467
#>  [8,] -2.45123127 -0.6978045  0.04993604  0.70784522
#>  [9,] -1.89533742  1.2601492 -0.70967190  1.87810360
#> [10,]  0.09237754  1.2786321  0.12774626 -0.03098862