spatPlot3D

Visualize cells according to spatial coordinates

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

Arguments

Value

See also