Set giotto subobjects into giotto object
Usage
# S4 method for class 'giotto,list'
setGiotto(gobject, x, verbose = TRUE, ...)
# S4 method for class 'giotto,cellMetaObj'
setGiotto(gobject, x, ...)
# S4 method for class 'giotto,featMetaObj'
setGiotto(gobject, x, ...)
# S4 method for class 'giotto,exprObj'
setGiotto(gobject, x, ...)
# S4 method for class 'giotto,giottoPoints'
setGiotto(gobject, x, ...)
# S4 method for class 'giotto,giottoPolygon'
setGiotto(gobject, x, ...)
# S4 method for class 'giotto,dimObj'
setGiotto(gobject, x, ...)
# S4 method for class 'giotto,spatLocsObj'
setGiotto(gobject, x, ...)
# S4 method for class 'giotto,spatEnrObj'
setGiotto(gobject, x, ...)
# S4 method for class 'giotto,nnNetObj'
setGiotto(gobject, x, ...)
# S4 method for class 'giotto,spatialNetworkObj'
setGiotto(gobject, x, ...)
# S4 method for class 'giotto,giottoLargeImage'
setGiotto(gobject, x, ...)
# S4 method for class 'giotto,giottoImage'
setGiotto(gobject, x, ...)See also
Other functions to set data in giotto object:
setCellMetadata(),
setDimReduction(),
setExpression(),
setFeatureInfo(),
setFeatureMetadata(),
setGiottoImage(),
setMultiomics(),
setNearestNetwork(),
setPolygonInfo(),
setSpatialEnrichment(),
setSpatialGrid(),
setSpatialLocations(),
setSpatialNetwork(),
set_multiomics()
Examples
g <- createGiottoObject()
#> 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_expression <- GiottoData::loadSubObjectMini("exprObj")
setGiotto(gobject = g, x = g_expression)
#> Setting expression [aggregate][rna] normalized
#> An object of class giotto
#> >Active spat_unit: aggregate
#> >Active feat_type: rna
#> dimensions : 337, 462 (features, cells)
#> [SUBCELLULAR INFO]
#> [AGGREGATE INFO]
#> expression -----------------------
#> [aggregate][rna] normalized
#>
#>
#> Use objHistory() to see steps and params used