plotStatDelaunayNetwork: plotStatDelaunayNetwork

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

Plots network statistics for a Delaunay network..

Usage

plotStatDelaunayNetwork(
  gobject,
  method = c("deldir", "delaunayn_geometry", "RTriangle"),
  dimensions = "all",
  maximum_distance = "auto",
  minimum_k = 0,
  options = "Pp",
  Y = TRUE,
  j = TRUE,
  S = 0,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "plotStatDelaunayNetwork",
  ...
)

Arguments

gobject	giotto object
method	package to use to create a Delaunay network
dimensions	which spatial dimensions to use (maximum 2 dimensions)
maximum_distance	distance cuttof for Delaunay neighbors to consider
minimum_k	minimum 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.
show_plot	show plots
return_plot	return ggplot object
save_plot	directly save the plot [boolean]
save_param	list of saving parameters, see showSaveParameters
default_save_name	default save name for saving, don't change, change save_name in save_param
...	Other parameters

Value

giotto object with updated spatial network slot

Examples

    plotStatDelaunayNetwork(gobject)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.