threejs_brain: Create a Threejs Brain and View it in Browsers

In threeBrain: Your Advanced 3D Brain Visualization

Create a Threejs Brain and View it in Browsers

Description

Create a Threejs Brain and View it in Browsers

Usage

threejs_brain(
  ...,
  .list = list(),
  width = NULL,
  height = NULL,
  background = "#FFFFFF",
  cex = 1,
  timestamp = TRUE,
  title = "",
  side_canvas = FALSE,
  side_zoom = 1,
  side_width = 250,
  side_shift = c(0, 0),
  side_display = TRUE,
  control_panel = TRUE,
  control_presets = NULL,
  control_display = TRUE,
  camera_center = c(0, 0, 0),
  camera_pos = c(500, 0, 0),
  start_zoom = 1,
  symmetric = 0,
  default_colormap = "Value",
  palettes = NULL,
  value_ranges = NULL,
  value_alias = NULL,
  show_inactive_electrodes = TRUE,
  surface_colormap = system.file("palettes", "surface", "ContinuousSample.json", package
    = "threeBrain"),
  voxel_colormap = system.file("palettes", "datacube2", "FreeSurferColorLUT.json",
    package = "threeBrain"),
  videos = list(),
  widget_id = "threebrain_data",
  tmp_dirname = NULL,
  debug = FALSE,
  enable_cache = FALSE,
  token = NULL,
  controllers = list(),
  browser_external = TRUE,
  global_data = list(),
  global_files = list(),
  qrcode = NULL,
  custom_javascript = NULL,
  show_modal = "auto",
  embed = FALSE
)

Arguments

..., .list	geometries inherit from AbstractGeom
width, height	positive integers. Width and height of the widget. By default width='100%', and height varies.
background	character, background color such as "#FFFFFF" or "white"
cex	positive number, relative text magnification level
timestamp	logical, whether to show time-stamp at the beginning
title	viewer title
side_canvas	logical, enable side cameras to view objects from fixed perspective
side_zoom	numerical, if side camera is enabled, zoom-in level, from 1 to 5
side_width	positive integer, side panel size in pixels
side_shift	integer of length two, side panel shift in pixels ('CSS style': top, left)
side_display	logical, show/hide side panels at beginning
control_panel	logical, enable control panels for the widget
control_presets	characters, presets to be shown in control panels
control_display	logical, whether to expand/collapse control UI at the beginning
camera_center	numerical, length of three, XYZ position where camera should focus at
camera_pos	XYZ position of camera itself, default (0, 0, 500)
start_zoom	numerical, positive number indicating camera zoom level
symmetric	numerical, default 0, color center will be mapped to this value
default_colormap	character, which color map name to display at startup
palettes	named list, names corresponds to color-map names if you want to change color palettes
value_ranges	named list, similar to palettes, value range for each values
value_alias	named list, legend title for corresponding variable
show_inactive_electrodes	logical, whether to show electrodes with no values
surface_colormap	a color map or its path generated by create_colormap(gtype="surface") to render surfaces vertices; see create_colormap for details.
voxel_colormap	a color map or its path generated by create_colormap(gtype="volume") to render volume such as atlases; see create_colormap for details.
videos	named list, names corresponds to color-map names, and items are generated from video_content
widget_id	character, internally used as unique identifiers for widgets; only use it when you have multiple widgets in one website
tmp_dirname	character path, internally used, where to store temporary files
debug	logical, internally used for debugging
enable_cache	whether to enable cache, useful when rendering the viewers repeatedly in shiny applications
token	unique character, internally used to identify widgets in 'JavaScript' 'localStorage'
controllers	list to override the settings, for example proxy$get_controllers()
browser_external	logical, use system default browser (default) or built-in one.
global_data, global_files	internally use, mainly to store orientation matrices and files.
qrcode	'URL' to show in the 'QR' code; can be a character string or a named list of 'url' and 'text' (hyper-reference text)
custom_javascript	customized temporary 'JavaScript' code that runs after ready state; available 'JavaScript' variables are: 'groups' input information about each group 'geoms' input information about each geometry 'settings' input information about canvas settings 'scene' 'threejs' scene object 'canvas' canvas object 'gui' controls data panel 'presets' preset 'gui' methods
show_modal	logical or "auto", whether to show a modal instead of direct rendering the viewers; designed for users who do not have 'WebGL' support; only used in shiny applications
embed	whether to try embedding the viewer in current run-time; default is false (will launch default web browser); set to true if running in 'rmarkdown' or 'quarto', or to see the viewer in 'RStudio' default panel.

Author(s)

Zhengjia Wang

Examples

if( interactive() ) {
library(threeBrain)

# Please use `download_N27` to download N27 Collins template brain
n27_path <- file.path(default_template_directory(), "N27")
if( dir.exists(n27_path) ) {

  brain <- threeBrain(path = n27_path, subject_code = "N27",
                             surface_types = c('pial', 'smoothwm'))
  print(brain)

  brain$plot(
    background = "#000000",
    controllers = list(
      'Voxel Type' = 'aparc_aseg',
      'Surface Type' = 'smoothwm',
      'Blend Factor' = 1,
      'Right Opacity' = 0.3,
      'Overlay Sagittal' = TRUE
    ),
    show_modal = TRUE
  )

}
}

threeBrain documentation built on April 4, 2025, 1:36 a.m.