insertCrossSectionSpatPlot3D#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/cross_section.R#L783

Description#

Visualize the meshgrid lines of cross section together with cells

Usage#

insertCrossSectionSpatPlot3D(
  gobject,
  spat_loc_name = "raw",
  crossSection_obj = NULL,
  name = NULL,
  spatial_network_name = "Delaunay_network",
  mesh_grid_color = "#1f77b4",
  mesh_grid_width = 3,
  mesh_grid_style = "dot",
  sdimx = "sdimx",
  sdimy = "sdimy",
  sdimz = "sdimz",
  show_other_cells = F,
  axis_scale = c("cube", "real", "custom"),
  custom_ratio = NULL,
  default_save_name = "spat3D_with_cross_section",
  ...
)

Arguments#

Argument

Description

gobject

giotto object

spat_loc_name

name of spatial locations

crossSection_obj

cross section object as alternative input. default = NULL.

name

name of virtual cross section to use

spatial_network_name

name of spatial network to use

mesh_grid_color

color for the meshgrid lines

mesh_grid_width

width for the meshgrid lines

mesh_grid_style

style for the meshgrid lines

sdimx

x-axis dimension name (default = ‘sdimx’)

sdimy

y-axis dimension name (default = ‘sdimy’)

sdimz

z-axis dimension name (default = ‘sdimy’)

show_other_cells

display not selected cells

axis_scale

axis_scale

custom_ratio

custom_ratio

default_save_name

default save name for saving, don’t change, change save_name in save_param

...

parameters for spatPlot3D

Details#

Description of parameters.

Value#

ggplot