createSpatialDelaunayNetwork#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_structures.R#L1067

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,
  ...
)

Arguments#

Argument

Description

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 boxplot graphics 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)

list()

Other additional parameters

Details#

Creates a spatial Delaunay network as explained in `delaunayn <#delaunayn>`__ (default), `deldir <#deldir>`__ , or `triangulate <#triangulate>`__ .

Value#

giotto object with updated spatial network slot