`insertCrossSectionGenePlot3D`¶

insertCrossSectionGenePlot3D

Description¶

Visualize cells and gene expression in a virtual cross section according to spatial coordinates

Usage¶

insertCrossSectionGenePlot3D(
  gobject,
  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,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "spatGenePlot3D_with_cross_section",
  ...
)

Arguments¶

Argument	Description
`gobject`	giotto object
`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
`show_plot`	show plots
`return_plot`	return ggplot object
`save_plot`	directly save the plot [boolean]
`save_param`	list of saving parameters from ``all_plots_save_function` <#allplotssavefunction>`_
`default_save_name`	default save name for saving, don’t change, change save_name in save_param
`...`	parameters for spatGenePlot3D

Details¶

Description of parameters.

Value¶

ggplot