insertCrossSectionGenePlot3D — insertCrossSectionGenePlot3D • Giotto

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

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

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
default_save_name: default save name for saving, don't change, change save_name in save_param
...: parameters for spatGenePlot3D

Value

ggplot

Details

Description of parameters.