Create a spatial Delaunay network

Create a spatial Delaunay network based on cell centroid physical distances.

Usage

createSpatialDelaunayNetwork(
  gobject,
  name = "Delaunay_network",
  spat_unit = NULL,
  feat_type = NULL,
  spat_loc_name = NULL,
  method = c("deldir", "delaunayn_geometry", "RTriangle"),
  dimensions = "all",
  maximum_distance = "auto",
  minimum_k = 0,
  options = "Pp",
  Y = TRUE,
  j = TRUE,
  S = 0,
  verbose = TRUE,
  return_gobject = TRUE,
  output = c("spatialNetworkObj", "data.table"),
  ...
)

Arguments

gobject

giotto object

name

name for spatial network (default = 'delaunay_network')

spat_unit

spatial unit

feat_type

feature type

spat_loc_name

name of spatial locations

method

package to use to create a Delaunay network

dimensions

which spatial dimensions to use. Use "sdimx" (spatial dimension x), "sdimy", "sdimz" respectively to refer to X (or the 1st), Y (or the 2nd) and Z(or the 3rd) dimension, see details. (default = all)

maximum_distance

distance cuttof for Delaunay neighbors to consider. If "auto", "upper whisker" value of the distance vector between neighbors is used; see the graphics::boxplot() documentation for more details.(default = "auto")

minimum_k

minimum number of neighbours if maximum_distance != NULL

options

(geometry) String containing extra control options for the underlying Qhull command; see the Qhull documentation for the available options. (default = 'Pp', do not report precision problems)

Y

(RTriangle) If TRUE prohibits the insertion of Steiner points on the mesh boundary.

j

(RTriangle) If TRUE jettisons vertices that are not part of the final triangulation from the output.

S

(RTriangle) Specifies the maximum number of added Steiner points.

verbose

be verbose

return_gobject

logical. return giotto object (default = TRUE)

output

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

...

Other additional parameters

Value

giotto object with updated spatial network slot

Details

Creates a spatial Delaunay network as explained in delaunayn (default), deldir, or triangulate.

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"

createSpatialDelaunayNetwork(g)
#> Delaunay_network has already been used, will be overwritten
#> > " Delaunay_network " already exists and will be replaced with new spatial
#>  network
#> 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