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Get multiomics integration results

Source: R/slot_accessors.R
get_multiomics.Rd

Get a multiomics integration result from a Giotto object

Usage

get_multiomics(
  gobject,
  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: getMultiomics(), setMultiomics(), set_multiomics()

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

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"
)

get_multiomics(gobject = g, spat_unit = "cell", feat_type = "rna_protein")
#>             [,1]        [,2]       [,3]        [,4]         [,5]         [,6]
#>  [1,]  1.6942495 -0.03878426 -0.1093242  0.38788578  0.449872371  0.485255132
#>  [2,] -0.7301832 -0.68491767  0.9468597 -1.01600463 -0.309074256  0.493486649
#>  [3,] -0.8628747 -0.26056907 -0.6209682 -0.99258532 -0.081790009 -0.029542086
#>  [4,] -0.6709940 -0.46362244 -2.1999743 -1.54756870  0.001140469 -1.363226303
#>  [5,] -0.5720964 -0.25088119  0.7251290  0.32035846 -0.932494155 -0.204966572
#>  [6,]  0.7021530 -0.11114805 -0.6148188  0.37105137 -0.404870001  0.822663111
#>  [7,] -1.5974143 -0.06563187  0.5398814 -1.03140550 -0.949265398  0.007932113
#>  [8,] -0.3951814  1.19006726 -1.2928481 -0.78365784  0.621378777 -1.065901513
#>  [9,]  1.7543038  0.04508842  0.6189336 -0.99651782 -0.410902192  1.154397620
#> [10,] -0.6460922 -1.89658438 -0.8892309 -0.05743969  1.360461019  2.229126086
#>              [,7]        [,8]        [,9]       [,10]
#>  [1,]  0.45142168  0.33258723  2.22803457 -0.31157786
#>  [2,]  0.42418676 -0.55778122 -0.07541334 -1.38696731
#>  [3,] -0.34161993 -0.11197384 -0.21078185  0.12923355
#>  [4,]  0.38570273 -0.26470514  0.24297428  1.00573752
#>  [5,]  0.15879998 -1.20125184  0.97327496 -0.31017322
#>  [6,]  0.48956358 -0.92344928 -0.05287263  0.68550654
#>  [7,]  0.03790973  0.62227415  1.61197214 -1.41374378
#>  [8,] -0.38386887 -0.02858395 -1.03632874  0.76635545
#>  [9,]  0.16924513  0.11010681  0.38942392 -0.01258768
#> [10,]  0.02372518  0.38126421  0.52370902  0.13655541