create_crossSection_object: create_crossSection_object
In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

create_crossSection_object

R Documentation

create_crossSection_object

Description

create a crossSection object

Usage

create_crossSection_object(
  name = NULL,
  method = NULL,
  thickness_unit = NULL,
  slice_thickness = NULL,
  cell_distance_estimate_method = NULL,
  extend_ratio = NULL,
  plane_equation = NULL,
  mesh_grid_n = NULL,
  mesh_obj = NULL,
  cell_subset = NULL,
  cell_subset_spatial_locations = NULL,
  cell_subset_projection_locations = NULL,
  cell_subset_projection_PCA = NULL,
  cell_subset_projection_coords = NULL
)

Arguments

`name`	name of cress section object. (default = cross_sectino)
`method`	method to define the cross section plane.
`thickness_unit`	unit of the virtual section thickness. If "cell", average size of the observed cells is used as length unit. If "natural", the unit of cell location coordinates is used.(default = cell)
`slice_thickness`	thickness of slice
`cell_distance_estimate_method`	method to estimate average distance between neighobring cells. (default = mean)
`extend_ratio`	deciding the span of the cross section meshgrid, as a ratio of extension compared to the borders of the vitural tissue section. (default = 0.2)
`plane_equation`	a numerical vector of length 4, in the form of c(A,B,C,D), which defines plane Ax+By+Cz=D.
`mesh_grid_n`	numer of meshgrid lines to generate along both directions for the cross section plane.
`mesh_obj`	object that stores the cross section meshgrid information.
`cell_subset`	cells selected by the cross section
`cell_subset_spatial_locations`	locations of cells selected by the cross section
`cell_subset_projection_locations`	3D projection coordinates of selected cells onto the cross section plane
`cell_subset_projection_PCA`	pca of projection coordinates
`cell_subset_projection_coords`	2D PCA coordinates of selected cells in the cross section plane