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"
)
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