spatDimPlot3D#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_visuals.R#L7941

Description#

Visualize cells according to spatial AND dimension reduction coordinates in plotly mode

Usage#

spatDimPlot3D(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  plot_alignment = c("horizontal", "vertical"),
  dim_reduction_to_use = "umap",
  dim_reduction_name = "umap",
  dim1_to_use = 1,
  dim2_to_use = 2,
  dim3_to_use = 3,
  spat_loc_name = NULL,
  sdimx = "sdimx",
  sdimy = "sdimy",
  sdimz = "sdimz",
  spat_enr_names = NULL,
  show_NN_network = FALSE,
  nn_network_to_use = "sNN",
  network_name = "sNN.pca",
  nn_network_color = "lightgray",
  nn_network_alpha = 0.5,
  show_cluster_center = F,
  show_center_label = T,
  center_point_size = 4,
  label_size = 16,
  select_cell_groups = NULL,
  select_cells = NULL,
  show_other_cells = T,
  other_cell_color = "lightgrey",
  other_point_size = 1.5,
  cell_color = NULL,
  color_as_factor = T,
  cell_color_code = NULL,
  dim_point_size = 3,
  show_spatial_network = F,
  spatial_network_name = "Delaunay_network",
  spatial_network_color = "lightgray",
  spatial_network_alpha = 0.5,
  show_spatial_grid = F,
  spatial_grid_name = "spatial_grid",
  spatial_grid_color = NULL,
  spatial_grid_alpha = 0.5,
  spatial_point_size = 3,
  axis_scale = c("cube", "real", "custom"),
  custom_ratio = NULL,
  x_ticks = NULL,
  y_ticks = NULL,
  z_ticks = NULL,
  legend_text_size = 12,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "spatDimPlot3D"
)

Arguments#

Argument

Description

gobject

giotto object

spat_unit

spatial unit

feat_type

feature type

plot_alignment

direction to align plot

dim_reduction_to_use

dimension reduction to use

dim_reduction_name

dimension reduction name

dim1_to_use

dimension to use on x-axis

dim2_to_use

dimension to use on y-axis

dim3_to_use

dimension to use on z-axis

spat_loc_name

name for spatial locations

sdimx

= spatial dimension to use on x-axis

sdimy

= spatial dimension to use on y-axis

sdimz

= spatial dimension to use on z-axis

spat_enr_names

names of spatial enrichment results to include

show_NN_network

show underlying NN network

nn_network_to_use

type of NN network to use (kNN vs sNN)

network_name

name of NN network to use, if show_NN_network = TRUE

nn_network_color

color of nn network

nn_network_alpha

column to use for alpha of the edges

show_cluster_center

show the center of each cluster

show_center_label

provide a label for each cluster

center_point_size

size of the center point

label_size

size of the center label

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

cell_color

color for cells (see details)

color_as_factor

convert color column to factor

cell_color_code

named vector with colors

dim_point_size

size of points in dim. reduction space

show_spatial_network

show spatial network

spatial_network_name

name of spatial network to use

spatial_network_color

color of spatial network

spatial_network_alpha

alpha of spatial network

show_spatial_grid

show spatial grid

spatial_grid_name

name of spatial grid to use

spatial_grid_color

color of spatial grid

spatial_grid_alpha

alpha of spatial grid

spatial_point_size

size of spatial points

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

legend_text_size

size of legend

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

Details#

Description of parameters.

Value#

plotly

Seealso#

Other spatial and dimension reduction visualizations: `spatDimPlot2D <#spatdimplot2d>`__ , `spatDimPlot <#spatdimplot>`__