brainconn: Plots brains
In Ali-Mahzarnia/brainconn2: Plotting Tool for Brain Connectivity Data

View source: R/brainconn.R

brainconn

R Documentation

Plots brains

Description

brainconn plots and returns a ggraph object of plotted brain connectivity matrix..

Usage

brainconn(
  atlas,
  background = "ICBM152",
  view = "top",
  conmat = NULL,
  node.size = 4,
  node.color = "network",
  all.nodes = FALSE,
  edge.color = "black",
  edge.alpha = 0.8,
  edge.width = 1,
  edge.color.weighted = FALSE,
  labels = FALSE,
  show.legend = TRUE,
  thr = NULL,
  uthr = NULL,
  scale.edge.width = NULL,
  label.size = 1.5,
  label.edge.weight = FALSE,
  background.alpha = 1
)

Arguments

`background`	'ICBM152', currently the only background option
`view`	A sting to choose the view. Can be any of these: c("ortho", "top", "bottom", "left", "right")
`conmat`	A adjacency matrix. Can be binary, weights, directed or undirected. see example_* data.
`node.size`	A integer that determines the diameter of the nodes. Can also be a vector of integers with a length equal to the number of ROIs in the atlas
`node.color`	A string that sets the node color. e.g. "blue". If set to "network", then nodes will be colored according to the network column of the atlas
`all.nodes`	if `TRUE`, then all nodes will be shown be hemisphere without ticks. If `FALSE`, then only nodes with connecting edges will be shown.
`edge.color`	A string that sets the edge color. e.g. "blue".
`edge.alpha`	Number between 0-1 to set the transparency of the edges.
`edge.width`	Number to set the width of the edges.
`edge.color.weighted`	A boolean that applies when the conmat is weighted. if `TRUE`, then edges will be colored according to the weight `FALSE`, the edges will be sized according to weight.
`labels`	if `TRUE`, ROI labels for all visible nodes will be shown. If `FALSE`, then no labes will be shown.
`show.legend`	if `TRUE`, legend will be shown. If `FALSE`, then no legend will be shown.
`thr`	a optional value to set a threshold on the conmat (e.g. edges with a weighted value lower than the one set here will not be shown)
`uthr`	a optional value to set a upper threshold on the conmat (e.g. edges with a weighted value higher than the one set here will not be shown)
`scale.edge.width`	If `edge.color.weighted=FALSE`, you can use this rescale the edge.width according to weight. e.g. `scale.edge.width = c(1,3)`
`label.size`	If labels=TRUE then, `label.size` can can be set as in integer to control the size of the labels.
`label.edge.weight`	if `TRUE`, then the edge weight will be labels along the edge.
`background.alpha`	Number between 0-1 to set the transparency of the background.

Value

a ggraph object

Author(s)

Sidhant Chopra

Examples

library(brainconn)
x=matrix(0,84,84)
x[1:3,9:11]= 1:3 ;x[9:11,1:3]= 3:1
brainconn(atlas ="Desikan84", conmat=x,
          view="ortho", node.size =2,
          node.color = "pink",
          edge.width = 1, edge.color="blue",
          edge.alpha = 0.65,
          edge.color.weighted = T,
          scale.edge.width=T,
          labels = T,
          all.nodes =F,
          show.legend = T,
          label.size=3, background.alpha=1,
          label.edge.weight=F)

#In order to learn more about the Desikan84 Atlas added to the package run the following command:

library(brainconn)
Desikan84=as.data.frame(Desikan84);Desikan84

Ali-Mahzarnia/brainconn2 documentation built on Feb. 19, 2024, 4:16 a.m.