create_crossSection_object — create_crossSection

create a crossSection object

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