spatPlot3D: spatPlot3D

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

Visualize cells according to spatial coordinates

Usage

spatPlot3D(
  gobject,
  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

gobject	giotto object
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
default_save_name	default save name for saving, don't change, change save_name in save_param

Value

ggplot

See Also

Other spatial visualizations: spatPlot2D(), spatPlot()

Examples

    spatPlot3D(gobject)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.