createCrossSection#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/cross_section.R#L421

Description#

Create a virtual 2D cross section.

Usage#

createCrossSection(
  gobject,
  spat_loc_name = "raw",
  name = "cross_section",
  spatial_network_name = "Delaunay_network",
  thickness_unit = c("cell", "natural"),
  slice_thickness = 2,
  cell_distance_estimate_method = "mean",
  extend_ratio = 0.2,
  method = c("equation", "3 points", "point and norm vector",
    "point and two plane vectors"),
  equation = NULL,
  point1 = NULL,
  point2 = NULL,
  point3 = NULL,
  normVector = NULL,
  planeVector1 = NULL,
  planeVector2 = NULL,
  mesh_grid_n = 20,
  return_gobject = TRUE
)

Arguments#

Argument

Description

gobject

giotto object

spat_loc_name

name of spatial locations

name

name of cress section object. (default = cross_sectino)

spatial_network_name

name of spatial network object. (default = Delaunay_network)

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. default = 2

ce ll_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)

method

method to define the cross section plane. If equation, the plane is defined by a four element numerical vector (equation) in the form of c(A,B,C,D), corresponding to a plane with equation Ax+By+Cz=D. If 3 points, the plane is define by the coordinates of 3 points, as given by point1, point2, and point3. If point and norm vector, the plane is defined by the coordinates of one point (point1) in the plane and the coordinates of one norm vector (normVector) to the plane. If point and two plane vector, the plane is defined by the coordinates of one point (point1) in the plane and the coordinates of two vectors (planeVector1, planeVector2) in the plane. (default = equation)

equation

equation required by method “equation?.equations needs to be a numerical vector of length 4, in the form of c(A,B,C,D), which defines plane Ax+By+Cz=D.

point1

coordinates of the first point required by method “3 points?,“point and norm vector?, and “point and two plane vectors?.

point2

coordinates of the second point required by method “3 points?

point3

coordinates of the third point required by method “3 points?

normVector

coordinates of the norm vector required by method “point and norm vector?

planeVector1

coordinates of the first plane vector required by method “point and two plane vectors?

planeVector2

coordinates of the second plane vector required by method “point and two plane vectors?

mesh_grid_n

numer of meshgrid lines to generate along both directions for the cross section plane.

return_gobject

boolean: return giotto object (default = TRUE)

Details#

Creates a virtual 2D cross section object for a given spatial network object. The users need to provide the definition of the cross section plane (see method).

Value#

giotto object with updated spatial network slot