`spatPlot3D`¶

spatPlot3D

Description¶

Visualize cells according to spatial coordinates

Usage¶

spatPlot3D(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  sdimx = "sdimx",
  sdimy = "sdimy",
  sdimz = "sdimz",
  spat_enr_names = NULL,
  point_size = 3,
  cell_color = NULL,
  cell_color_code = NULL,
  select_cell_groups = NULL,
  select_cells = NULL,
  show_other_cells = T,
  other_cell_color = "lightgrey",
  other_point_size = 0.5,
  other_cell_alpha = 0.5,
  show_network = F,
  spatial_network_name = "Delaunay_network",
  network_color = NULL,
  network_alpha = 1,
  show_grid = F,
  spatial_grid_name = "spatial_grid",
  grid_color = NULL,
  grid_alpha = 1,
  title = "",
  show_legend = T,
  axis_scale = c("cube", "real", "custom"),
  custom_ratio = NULL,
  x_ticks = NULL,
  y_ticks = NULL,
  z_ticks = NULL,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "spat3D"
)

Arguments¶

Argument	Description
`gobject`	giotto object
`spat_unit`	spatial unit
`feat_type`	feature type
`sdimx`	x-axis dimension name (default = ‘sdimx’)
`sdimy`	y-axis dimension name (default = ‘sdimy’)
`sdimz`	z-axis dimension name (default = ‘sdimy’)
`spat_enr_names`	names of spatial enrichment results to include
`point_size`	size of point (cell)
`cell_color`	color for cells (see details)
`cell_color_code`	named vector with colors
`select_cell_groups`	select subset of cells/clusters based on cell_color parameter
`select_cells`	select subset of cells based on cell IDs
`show_other_cells`	display not selected cells
`other_cell_color`	color of not selected cells
`other_point_size`	size of not selected cells
`other_cell_alpha`	alpha of not selected cells
`show_network`	show underlying spatial network
`spatial_network_name`	name of spatial network to use
`network_color`	color of spatial network
`network_alpha`	opacity of spatial network
`show_grid`	show spatial grid
`spatial_grid_name`	name of spatial grid to use
`grid_color`	color of spatial grid
`grid_alpha`	opacity of spatial grid
`title`	title of plot
`show_legend`	show legend
`axis_scale`	the way to scale the axis
`custom_ratio`	customize the scale of the plot
`x_ticks`	set the number of ticks on the x-axis
`y_ticks`	set the number of ticks on the y-axis
`z_ticks`	set the number of ticks on the z-axis
`show_plot`	show plot
`return_plot`	return ggplot object
`save_plot`	directly save the plot [boolean]
`save_param`	list of saving parameters, see ``showSaveParameters` <#showsaveparameters>`_
`default_save_name`	default save name for saving, don’t change, change save_name in save_param

Value¶

ggplot

Seealso¶

Other spatial visualizations:: ``spatPlot2D` <#spatplot2d>`_ , ``spatPlot` <#spatplot>`_