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README.Rmd
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---
title: "Plotting tool for brain connectivity data"
author: "Sidhant Chopra"
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/img/README-",
echo = TRUE,
warning = FALSE,
message = FALSE
)
library(magrittr)
if (!require("processx")) install.packages("processx")
devtools::load_all(".")
```
# brainconn <img src="man/img/logo.png" align="right" alt="" width="180" />
<!-- badges: start -->
[](https://travis-ci.com/sidchop/brainconn)
[](https://ci.appveyor.com/project/sidchop/brainconn)
[](https://codecov.io/gh/sidchop/brainconn)
[](https://CRAN.R-project.org/package=brainconn)
[](https://www.tidyverse.org/lifecycle/#maturing)
<!-- badges: end -->
The purpose of this package is to allow for flexible, programmatic and interactive plotting of brain connectivity data within Rstudio - negating the need to swap to other visualization tools and allowing for reproducible integration of visualization with analysis scripts that are written in R.
The primary plotting functions: `brainconn()` and `brainconn3D()`. The primary user input into these function is a connectivity matrix. Several brain atlases come pre-installed and users can also provide a custom atlas (see vignette).
The `brainconn()` function allows users to input a binary/weighted and directed/non-directed (i.e. symmetric) connectivity matrix which can be plotted onto MNI coordinates using [ggraph](https://github.com/ggraph).
The `brainconn3D()` allows users to input a binary and non-directed connectivity matrix which is plotted in a 3D and interactive way using [plottly](https://github.com/plotly).
The atlases currently included with in the package can be listed using the `list_atlases()` function: `aal116`, `aal90`, `craddock200`, `dk68`, `dk82_aspree`, `dkt62`, `gordon_333`, `shen_268`, `shen_368`, `schaefer1000_n7`, `schaefer1000_n17`, `schaefer300_n7`, `schaefer300_n17` (and all other iterations of the schaefer atlases). Custom atlases can be easily added as long as you have centroid coordinates in MNI space, see [vignette](https://sidchop.github.io/brainconn/articles/brainconn.html). The `check_atlas()` function checks that custom atlases meet the requirements of the plotting functions.
## Installation
The package can be installed using devtools.
```{r eval=F}
install.packages("remotes")
remotes::install_github("sidchop/brainconn")
```
The functions are now installed, and you may load them when you want to use them.
## Use
The package also has a vignette, to help you get started. You can access it [here](https://sidchop.github.io/brainconn/articles/brainconn.html), or via R:
```{r, out.width='50%', eval=FALSE}
library(brainconn)
vignette("brainconn")
```
The primary user input is a connectivity matrix (`conmat`).
```{r, out.width='50%', echo=T, warning=F, eval=F}
brainconn(atlas ="schaefer300_n7", conmat=example_unweighted_undirected, view="ortho")
```
```{r, echo = FALSE,warning=F, error=F}
knitr::include_graphics("man/figures/000010.png")
```
Modifiable features for `brainconn` include: `view`, `node.size`, `node.color`, `edge.width`, `edge.color`, `edge.alpha`, `background.alpha`, `labels` and others (see vignette)
```{r, results = 'hide', eval=F, echo=T, warning=F}
x <- example_unweighted_undirected
p <- brainconn3D(atlas ="schaefer300_n7", conmat=x, show.legend = F)
p
```
Included below is a gif of the interactive output (see [vignette](https://sidchop.github.io/brainconn/articles/brainconn.html) for more information):
```{r, echo = FALSE,warning=F, error=F}
knitr::include_graphics("man/img/README-gif.gif")
```
Modifiable features for `brainconn3D` include: `node.size`, `node.color`, `edge.width`, `edge.color`, `adge.alpha`, `background.alpha`, `labels` and others (see [vignette](https://sidchop.github.io/brainconn/articles/brainconn.html))
### Report bugs or requests
Don't hesitate to ask for support or new features using [github issues](https://github.com/sidchop/brainconn).
### Other R packages you might be intrested in:
* [ggseg](https://github.com/LCBC-UiO/ggseg) & [ggseg3D](https://github.com/LCBC-UiO/ggseg3d): Plotting tool for brain atlases, in ggplot/plotly
* [brainGraph](https://github.com/cwatson/brainGraph): Graph theory analysis of brain MRI data
* [fsbrain](https://github.com/dfsp-spirit/fsbrain): Provides high-level functions to access (read and write) and visualize surface-based brain morphometry data (e.g. cortical thickness) for individual subjects and groups.
* [NBR](https://github.com/zchuri/NBR/): Network Based R-statistics for Mixed Effects Models
* [fslr](https://github.com/muschellij2/fslr): FSL-R Interface package
### Citations
If you end up using `brainconn()` in a publication, please cite our paper, for which brainconn was created : Sidhant Chopra, Loïc Labache, Elvisha Dhamala, Edwina R Orchard, Avram Holmes (2023). *A Practical Guide for Generating Reproducible and Programmatic Neuroimaging Visualizations* ApertureNeuro. \
https://doi.org/10.52294/001c.85104