createSpatialKNNnetwork

Create a spatial knn network.

Usage

createSpatialKNNnetwork(
  gobject,
  method = "dbscan",
  spat_unit = NULL,
  feat_type = NULL,
  spat_loc_name = NULL,
  dimensions = "all",
  name = "knn_network",
  k = 4,
  maximum_distance = NULL,
  minimum_k = 0,
  verbose = FALSE,
  return_gobject = TRUE,
  output = c("spatialNetworkObj", "data.table"),
  ...
)

Arguments

gobject

giotto object

method

method to create kNN network

spat_unit

spatial unit

feat_type

feature type

spat_loc_name

name of spatial locations

dimensions

which spatial dimensions to use (default = all)

name

name for spatial network (default = 'spatial_network')

k

number of nearest neighbors based on physical distance

maximum_distance

distance cuttof for nearest neighbors to consider for kNN network

minimum_k

minimum nearest neigbhours if maximum_distance != NULL

verbose

verbose

return_gobject

boolean: return giotto object (default = TRUE)

output

character. Object type to return spatial network as when return_gobject = FALSE. (default: 'spatialNetworkObj')

...

additional arguments to the selected method function

Value

giotto object with updated spatial network slot

dimensions: default = 'all' which takes all possible dimensions. Alternatively you can provide a character vector that specififies the spatial dimensions to use, e.g. c("sdimx', "sdimy") or a numerical vector, e.g. 2:3

maximum_distance: to create a network based on maximum distance only, you also need to set k to a very high value, e.g. k = 100

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"

createSpatialKNNnetwork(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 knn_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