Set a NN-network for a Giotto object
Usage
setNearestNetwork(
gobject,
x,
spat_unit = NULL,
feat_type = NULL,
nn_type = "sNN",
name = "sNN.pca",
provenance = NULL,
verbose = TRUE,
initialize = TRUE,
...
)Arguments
- gobject
giotto object
- x
nnNetObj or list of nnNetObj. Passing NULL will remove a specified set of nearest neighbor network information from the gobject
- spat_unit
spatial unit (e.g. "cell")
- feat_type
feature type (e.g. "rna", "dna", "protein")
- nn_type
"kNN" or "sNN"
- name
name of NN network to be used yet supported.
- provenance
provenance information (optional)
- verbose
be verbose
- initialize
(default = FALSE) whether to initialize the gobject before returning
- ...
additional params to pass
See also
Other expression space nearest network accessor functions:
getNearestNetwork()
Other functions to set data in giotto object:
setCellMetadata(),
setDimReduction(),
setExpression(),
setFeatureInfo(),
setFeatureMetadata(),
setGiotto(),
setGiottoImage(),
setMultiomics(),
setPolygonInfo(),
setSpatialEnrichment(),
setSpatialGrid(),
setSpatialLocations(),
setSpatialNetwork(),
set_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
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#> "/usr/share/miniconda/envs/giotto_env/bin/python"
dimred <- getNearestNetwork(gobject = g)
#> The NN network type was not specified, default to the
#> first: "sNN"
#> The NN network name was not specified, default to the
#> first: "sNN.pca"
setNearestNetwork(gobject = g, x = dimred)
#> > 'sNN.pca' already exists and will be replaced with
#> new nearest neighbor network
#> Setting nearest neighbor network [cell][rna] sNN.pca
#> An object of class giotto
#> >Active spat_unit: cell
#> >Active feat_type: rna
#> dimensions : 634, 624 (features, cells)
#> [SUBCELLULAR INFO]
#> polygons : cell
#> [AGGREGATE INFO]
#> expression -----------------------
#> [cell][rna] raw normalized scaled
#> spatial locations ----------------
#> [cell] raw
#> spatial networks -----------------
#> [cell] Delaunay_network spatial_network
#> spatial enrichments --------------
#> [cell][rna] cluster_metagene DWLS
#> dim reduction --------------------
#> [cell][rna] pca custom_pca umap custom_umap tsne
#> nearest neighbor networks --------
#> [cell][rna] sNN.pca custom_NN
#> attached images ------------------
#> images : alignment image
#>
#>
#> Use objHistory() to see steps and params used