Plots brains — brainconn • brainconn

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

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,
  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.
background.alpha	Number between 0-1 to set the transparency of the background.

Value

a ggraph object

Author

Sidhant Chopra

Examples

library(brainconn)
x <- example_unweighted_undirected
brainconn(atlas ="schaefer300_n7", conmat=x, node.size = 3, view="ortho")
#> Coordinate system already present. Adding new coordinate system, which will replace the existing one.