brainconn 
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 according to MNI coordinates.
The brainconn3D() allows users to input a binary and non-directed connectivity matrix which is plotted in a 3D and interactive way using plottly.
The atlases currently included with in the packaage can be listed using the list_atlases() function: aal116, aal90, craddock200, dk68, dk82_aspree, dkt62, gordon_333, schaefer1000_n7, schaefer300_17_cog_lang, schaefer300_n7, shen_268, shen_368. Custom atlases can be easily added as long as you have centroid coordinates in MNI space, see vignette. The check_atlas() function checks that custom atlases meet the requirements of the plotting functions.
Installation
The package can be installed using devtools.
install.packages("remotes")
remotes::install_github("sidchop/brainconn", build_vignettes = TRUE)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, or via R:
library(brainconn)
vignette("brainconn")The primary user input is a connectivity matrix (conmat).
brainconn(atlas ="schaefer300_n7", conmat=example_unweighted_undirected)
Modifiable features for brainconn include: view, node.size, node.color, edge.width, edge.color, edge.alpha, background.alpha, labels and others (see vignette)
x <- example_unweighted_undirected
p <- brainconn3D(atlas ="Stages_melbBrain", conmat=x, show.legend = F)
pIncluded below is a screenshot of the interactive output:
Modifiable features for brainconn3D include: node.size, node.color, edge.width, edge.color, adge.alpha, background.alpha, labels and others (see vignette)
Report bugs or requests
Don’t hesitate to ask for support or new features using github issues.