Add a network layout for a selected nearest neighbor network
Usage
addNetworkLayout(
gobject,
spat_unit = NULL,
feat_type = NULL,
nn_network_to_use = "sNN",
network_name = "sNN.pca",
layout_type = c("drl"),
options_list = NULL,
layout_name = "layout",
return_gobject = TRUE
)Arguments
- gobject
giotto object
- spat_unit
spatial unit
- feat_type
feature type
- nn_network_to_use
kNN or sNN
- network_name
name of NN network to be used
- layout_type
layout algorithm to use
- options_list
list of options for selected layout
- layout_name
name for layout
- return_gobject
boolean: return giotto object (default = TRUE)
Details
This function creates layout coordinates based on the provided
kNN or sNN.
Currently only the force-directed graph layout "drl",
see layout_with_drl, is implemented.
This provides an alternative to tSNE or UMAP based visualizations.
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
addNetworkLayout(g)
#> 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