ggseg3d

ggseg3d R package for visualising brain atlases through plotly

https://github.com/ggseg/ggseg3d

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
○
.zenodo.json file
○
DOI references
○
Academic publication links
✓
Committers with academic emails
1 of 6 committers (16.7%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (20.4%) to scientific vocabulary

Last synced: 11 months ago · JSON representation

Repository

ggseg3d R package for visualising brain atlases through plotly

Basic Info

Host: GitHub
Owner: ggseg
License: other
Language: R
Default Branch: master
Homepage: https://ggseg.github.io/ggseg3d/
Size: 530 MB

Statistics

Stars: 38
Watchers: 2
Forks: 11
Open Issues: 8
Releases: 1

Created over 6 years ago · Last pushed 12 months ago

Metadata Files

Readme Changelog License

README.Rmd

---
output: github_document
---

```{r, include = FALSE}
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  

[![Coverage status](https://codecov.io/gh/ggseg/ggseg3d/branch/master/graph/badge.svg)](https://codecov.io/gh/ggseg/ggseg3d)
[![CRAN status](https://www.r-pkg.org/badges/version/ggseg3d)](https://CRAN.R-project.org/package=ggseg3d)
[![downloads](https://cranlogs.r-pkg.org/badges/last-month/ggseg?color=blue)](https://r-pkg.org/pkg/ggseg)
[![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html)
[![R-CMD-check](https://github.com/LCBC-UiO/ggseg3d/workflows/R-CMD-check/badge.svg)](https://github.com/LCBC-UiO/ggseg3d/actions)


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](https://ggseg.github.io/ggsegExtra/).

## Installation


ggseg3d can be installed from CRAN with:

```{r, eval = FALSE}
install.packages("ggseg3d")
```


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

```{r eval = FALSE}
# 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.

```{r eval=F}
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](https://ggseg.github.io/ggseg3d/articles/ggseg3d.html), or via R:

```{r eval=F}
library(ggseg3d)
vignette("ggseg3d")
```

```{r results='hide'}
p <- ggseg3d(atlas=dk_3d) %>% 
  remove_axes() %>% 
  pan_camera("right lateral")
```
```{r, echo=FALSE}
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")
```


```{r results = 'hide'}
p <- ggseg3d(atlas=aseg_3d) %>% 
  add_glassbrain() %>% 
  remove_axes() %>% 
  pan_camera("right lateral")
```
```{r, echo = FALSE}
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](https://github.com/ggseg/ggseg3d/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

Owner

Name: ggseg - Lifebrain EU - LCBC UiO
Login: ggseg
Kind: organization
Location: Oslo, Norway

Website: https://www.lifebrain.uio.no/
Twitter: LifebrainEU
Repositories: 6
Profile: https://github.com/ggseg

ggseg-suite packages from the Lifebrain EU project lead by Center of Lifespan Changes in Brain and Cogntion - UiO

GitHub Events

Total

Issues event: 5
Watch event: 8
Issue comment event: 8
Pull request review event: 2
Pull request review comment event: 2
Pull request event: 1
Fork event: 2

Last Year

Issues event: 5
Watch event: 8
Issue comment event: 8
Pull request review event: 2
Pull request review comment event: 2
Pull request event: 1
Fork event: 2

Committers

Last synced: over 2 years ago

All Time

Total Commits: 194
Total Committers: 6
Avg Commits per committer: 32.333
Development Distribution Score (DDS): 0.124

Past Year

Commits: 1
Committers: 1
Avg Commits per committer: 1.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Athanasia Monika Mowinckel	a**l@p**o	170
Bernie Gray	b**3@g**m	9
muschellij2	m**2@g**m	9
Athanasia Monika Mowinckel	A****o	3
didacvp	3****p	2
Paul Brennan	b**f@g**m	1

Committer Domains (Top 20 + Academic)

psykologi.uio.no: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time

Total issues: 24
Total pull requests: 3
Average time to close issues: 5 months
Average time to close pull requests: 7 months
Total issue authors: 22
Total pull request authors: 2
Average comments per issue: 2.67
Average comments per pull request: 0.67
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 4
Pull requests: 2
Average time to close issues: about 11 hours
Average time to close pull requests: N/A
Issue authors: 4
Pull request authors: 1
Average comments per issue: 1.0
Average comments per pull request: 0.5
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

drmowinckels (3)
MarynaPolyakova (1)
conchobha (1)
jaromilfrossard (1)
narunpat (1)
Keikokunitoki (1)
zhangjb35 (1)
KBMD (1)
mgreen-neura (1)
ryssamoffat (1)
theyaneshj17 (1)
monicathieu (1)
bertram0611 (1)
ckelly5 (1)
alicarogojin (1)

Pull Request Authors

monicathieu (2)
muschellij2 (1)

Top Labels

Issue Labels

enhancement (2) wontfix (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 382 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 1
Total maintainers: 1

cran.r-project.org: ggseg3d

Tri-Surface Mesh Plots for Brain Atlases

Homepage: https://github.com/ggseg/ggseg3d/
Documentation: http://cran.r-project.org/web/packages/ggseg3d/ggseg3d.pdf
License: MIT + file LICENSE
Latest release: 1.6.3
published about 5 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 382 Last month

Rankings

Forks count: 7.3%

Stargazers count: 10.3%

Average: 21.0%

Dependent repos count: 23.9%

Dependent packages count: 28.7%

Downloads: 35.0%

Maintainers (1)

a.m.mowinckel@psykologi.uio.no

Last synced: 11 months ago

Dependencies

DESCRIPTION cran

R >= 2.10 depends
dplyr * imports
magrittr * imports
plotly * imports
scales * imports
tidyr * imports
utils * imports
covr * suggests
devtools * suggests
knitr * suggests
processx * suggests
rmarkdown * suggests
spelling * suggests
testthat >= 2.1.0 suggests

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

ggseg3d

Science Score: 23.0%

Repository

Basic Info

Statistics

Metadata Files

README.Rmd

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

cran.r-project.org: ggseg3d

Rankings

Maintainers (1)

Dependencies