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
)name of cross section object. (default = cross_section)
method to define the cross section plane.
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)
thickness of slice
method to estimate average distance between neighboring cells. (default = mean)
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)
a numerical vector of length 4, in the form of c(A,B,C,D), which defines plane Ax+By+Cz=D.
number of meshgrid lines to generate along both directions for the cross section plane.
object that stores the cross section meshgrid information.
cells selected by the cross section
locations of cells selected by the cross section
3D projection coordinates of selected cells onto the cross section plane
pca of projection coordinates
2D PCA coordinates of selected cells in the cross section plane
crossSection object