addNetworkLayout

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)

Value

giotto object with updated layout for selected NN network

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
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/share/miniconda/envs/giotto_env/bin/python"

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