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:
getDimReduction()
,
getExpression()
,
getFeatureInfo()
,
getGiottoImage()
,
getNearestNetwork()
,
getPolygonInfo()
,
getSpatialEnrichment()
,
getSpatialGrid()
,
getSpatialLocations()
,
getSpatialNetwork()
,
get_NearestNetwork()
,
get_dimReduction()
,
get_feature_info()
,
get_giottoImage()
,
get_multiomics()
,
get_polygon_info()
,
get_spatialGrid()
,
get_spatialNetwork()
,
get_spatial_enrichment()
,
get_spatial_locations()
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"
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,] -0.701836993 0.90639045 1.6667728 -1.25745550 0.37969672 -0.2013585
#> [2,] 0.573351259 -0.77007572 1.0805134 -0.27499746 0.81051411 -1.7947501
#> [3,] 0.653506513 -0.10392922 1.0956876 1.18512009 0.16798153 -1.5936760
#> [4,] 1.102562583 -0.59883015 -0.8235445 0.03108054 -0.82634150 -0.5880921
#> [5,] -0.331979510 0.86307592 -0.7896969 -0.20427061 0.48015487 -2.4436502
#> [6,] -0.006015914 1.53498056 -2.2300375 -1.34758305 -0.22734637 0.8733072
#> [7,] 0.542548136 -0.07677495 1.2682960 0.32840023 -0.38144334 -1.5700947
#> [8,] 1.073179083 0.36398407 0.7477098 1.50785612 -0.51130892 1.2064433
#> [9,] 0.431113801 0.80003990 0.2902944 0.51282324 1.61615062 -0.6020315
#> [10,] 0.899647924 -1.51114608 -0.2336790 0.27261523 0.05862038 0.6160790
#> [,7] [,8] [,9] [,10]
#> [1,] -0.29940886 0.61040765 0.21277709 -0.43014614
#> [2,] -0.54314989 0.86164700 -0.36930863 -0.23013339
#> [3,] -0.11165896 0.88285986 -0.10648446 1.82750672
#> [4,] -0.59879136 0.25782948 -0.52105633 1.63416402
#> [5,] -0.64283303 -2.41919619 -0.31239384 -0.30347819
#> [6,] -2.18494492 0.98255604 -1.73132386 0.05761964
#> [7,] 0.11409361 0.73347719 1.46947149 -0.50750744
#> [8,] 0.01148282 0.76860157 0.01044213 -1.61633811
#> [9,] 0.35329552 -0.01777067 0.40827683 0.89181656
#> [10,] 2.29670311 -1.10088452 1.70418504 -0.03268551