Create a spatial network based on cell centroid physical distances.

createSpatialNetwork( gobject, name = NULL, dimensions = "all", method = c("Delaunay", "kNN"), delaunay_method = c("deldir", "delaunayn_geometry", "RTriangle"), maximum_distance_delaunay = "auto", options = "Pp", Y = TRUE, j = TRUE, S = 0, minimum_k = 0, knn_method = "dbscan", k = 4, maximum_distance_knn = NULL, verbose = F, return_gobject = TRUE, ... )

gobject | giotto object |
---|---|

name | name for spatial network (default = 'spatial_network') |

dimensions | which spatial dimensions to use (default = all) |

method | which method to use to create a spatial network. (default = Delaunay) |

delaunay_method | Delaunay method to use |

maximum_distance_delaunay | distance cuttof for nearest neighbors to consider for Delaunay network |

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. |

minimum_k | minimum nearest neigbhours if maximum_distance != NULL |

knn_method | method to create kNN network |

k | number of nearest neighbors based on physical distance |

maximum_distance_knn | distance cuttof for nearest neighbors to consider for kNN network |

verbose | verbose |

return_gobject | boolean: return giotto object (default = TRUE) |

... | Additional parameters for the selected function |

giotto object with updated spatial network slot

Creates a spatial network connecting single-cells based on their physical distance to each other. For Delaunay method, neighbors will be decided by delaunay triangulation and a maximum distance criteria. For kNN method, number of neighbors can be determined by k, or maximum distance from each cell with or without setting a minimum k for each cell.

**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