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 cross section object. (default = cross_section)

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 neighboring cells. (default = mean)

extend_ratio

deciding the span of the cross section meshgrid, as a ratio of extension compared to the borders of the virtual 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

number 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

Value

crossSection object