createSpatialDelaunayNetwork: Create a spatial Delaunay network

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Create a spatial Delaunay network

Description

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 = T,
  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 wisker" value of the distance vector between neighbors is used; see the boxplotgraphics documentation for more details.(default = "auto")
minimum_k	minimum number of neigbhours if maximum_distance != NULL
options	(geometry) String containing extra control options for the underlying Qhull command; see the Qhull documentation (../doc/qhull/html/qdelaun.html) 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	verbose
return_gobject	boolean: return giotto object (default = TRUE)
output	object type to return spatial network as when return_gobject = FALSE. (default: 'spatialNetworkObj')
...	Other additional parameters

Details

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

Value

giotto object with updated spatial network slot

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.