spatPlot3D#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_visuals.R#L7741

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 `showSaveP arameters <#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>`__