In LCBC-UiO/ggseg3d: Tri-Surface Mesh Plots for Brain Atlases

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/img/README-",
  echo = TRUE
)
library(magrittr)
library(ggseg3d)
if (!require("processx")) install.packages("processx")

ggseg3d

This package mainly contains a plotting function ggseg3d and data.frames of different brain atlases for plotting. Plotting results of analyses on regions or networks often involves swapping between statistical tools, like R and Matlab, and software for brain imaging to correctly visualise analysis results.

This package aims to make it possible to plot results directly through R.

Atlases

There are currently four atlases available in the package:

1. dk_3d - Desikan-Killiany atlas (aparc).
2. aseg_3d - Automatic sub-cortical segmentation.

If you want to create your own custom atlas or discover other compatible atlases, please see the companion package ggsegExtra.

Installation

ggseg3d can be installed from CRAN with:

install.packages("ggseg3d")

We recommend installing {ggsegExtra} through the ggseg r-universe.

# Enable this universe
options(repos = c(
    ggseg = 'https://ggseg.r-universe.dev',
    CRAN = 'https://cloud.r-project.org'))

# Install some packages
install.packages('ggseg3d')

The package can be installed using {remotes}. The package includes some large datasets for the brain coordinates. Please be patient during download and install, it will take some time.

install.packages("remotes")
remotes::install_github("ggseg/ggseg3d", build_vignettes = TRUE)

The functions are now installed, and you may load them when you want to use them. All functions are documented in standard R fashion.

Use

The package also has a vignette, to help you get started using it. You can access it here, or via R:

library(ggseg3d)
vignette("ggseg3d")

p <- ggseg3d(atlas=dk_3d) %>% 
  remove_axes() %>% 
  pan_camera("right lateral")

p <- p %>% 
  plotly::add_annotations( text="Screen capture",
                  legendtitle=TRUE, showarrow=FALSE,
                  font = list(color = 'darkgrey',
                              family = 'sans serif',
                              size = 50)) 
plotly::orca(p, "man/img/README-dk_3d-plot.png")
knitr::include_graphics("man/img/README-dk_3d-plot.png")

p <- ggseg3d(atlas=aseg_3d) %>% 
  add_glassbrain() %>% 
  remove_axes() %>% 
  pan_camera("right lateral")

p <- p %>% 
  plotly::add_annotations( text="Screen capture",
                  legendtitle=TRUE, showarrow=FALSE,
                  font = list(color = 'darkgrey',
                              family = 'sans serif',
                              size = 50)) 
plotly::orca(p, "man/img/README-aseg_3d-plot.png")
knitr::include_graphics("man/img/README-aseg_3d-plot.png")

Report bugs or requests

Don't hesitate to ask for support using github issues, or requesting new atlases. While we would love getting help in creating new atlases, you may also request atlases through the issues, and we will try to get to it.

Funding

This tool is partly funded by:

EU Horizon 2020 Grant: Healthy minds 0-100 years: Optimising the use of European brain imaging cohorts (Lifebrain).

Grant agreement number: 732592.

Call: Societal challenges: Health, demographic change and well-being

LCBC-UiO/ggseg3d documentation built on Oct. 24, 2023, 3:49 a.m.