Set giotto polygon spatVector for features
Arguments
- gobject
giotto object
- x
giottoPoints object or list of giottoPoints to set. Passing NULL will remove the specified giottoPoints object from the giotto object
- feat_type
feature type (e.g. "rna", "dna", "protein")
- verbose
be verbose
- initialize
(default = FALSE) whether to initialize the gobject before returning
- ...
additional params to pass
See also
Other feature info data accessor functions:
getFeatureInfo()
Other functions to set data in giotto object:
setCellMetadata(),
setDimReduction(),
setExpression(),
setFeatureMetadata(),
setGiotto(),
setGiottoImage(),
setMultiomics(),
setNearestNetwork(),
setPolygonInfo(),
setSpatialEnrichment(),
setSpatialGrid(),
setSpatialLocations(),
setSpatialNetwork(),
set_multiomics()
Examples
g <- GiottoData::loadGiottoMini("vizgen")
#> 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"
featinfo <- getFeatureInfo(g, return_giottoPoints = TRUE)
setFeatureInfo(gobject = g, x = featinfo)
#> > " rna " already exists and will be
#> replaced with new giotto points
#> Setting feature info [rna]
#> An object of class giotto
#> >Active spat_unit: z0
#> >Active feat_type: rna
#> dimensions : 337, 498 (features, cells)
#> [SUBCELLULAR INFO]
#> polygons : z0 z1 aggregate
#> features : rna
#> [AGGREGATE INFO]
#> expression -----------------------
#> [z0][rna] raw
#> [z1][rna] raw
#> [aggregate][rna] raw normalized scaled pearson
#> spatial locations ----------------
#> [z0] raw
#> [z1] raw
#> [aggregate] raw
#> spatial networks -----------------
#> [aggregate] Delaunay_network kNN_network
#> spatial enrichments --------------
#> [aggregate][rna] cluster_metagene
#> dim reduction --------------------
#> [aggregate][rna] pca umap tsne
#> nearest neighbor networks --------
#> [aggregate][rna] sNN.pca
#> attached images ------------------
#> images : 4 items...
#>
#>
#> Use objHistory() to see steps and params used