ANTsR (version 0.4.0)

plotBasicNetwork: Simple plotBasicNetwork function.

Description

takes an object output from renderSurfaceFunction and a list of centroids and plots the centroid network over the rendering object

Usage

plotBasicNetwork(centroids, brain, weights = NA, edgecolors = 0,
  nodecolors = "blue", nodetype = "s", scaling = c(0, 0), lwd = 2,
  radius = NA, showOnlyConnectedNodes = TRUE)

Arguments

centroids

input matrix of size number of 3D points ( in rows ) by 3 ( in columns )

brain

input rendering object which is output of renderSurfaceFunction or a function derived from renderSurfaceFunction

weights

edge weights

edgecolors

a color(map) for edges

nodecolors

a color(map) for nodes

nodetype

sphere or other node type

scaling

controls functional range

lwd

line width

radius

for nodes

showOnlyConnectedNodes

boolean

Value

None

Examples

# NOT RUN {
# }
# NOT RUN {
# more complete example
  mnit<-getANTsRData("mni")
  mnit<-antsImageRead(mnit)
  mnia<-getANTsRData("mnia")
  mnia<-antsImageRead(mnia)
  mnit<-thresholdImage( mnit, 1, max(mnit) )
  mnit<-iMath(mnit,"FillHoles")
  cnt<-getCentroids( mnia, clustparam = 0 )
  aalcnt<-cnt[1:90,1:3]
  brain<-renderSurfaceFunction( surfimg =list( mnit ) , alphasurf=0.1 ,smoothsval = 1.5 )
  testweights<-matrix( rep( 0, 90*90 ) ,nrow=90)
  testweights[31,37]<-1  # ant cingulate to hipp
  testweights[31,36]<-2  # ant cingulate to post cingulate
  testweights[11,65]<-3  # broca to angular
  plotBasicNetwork( centroids = aalcnt , brain , weights=testweights )
  id<-rgl::par3d('userMatrix')
  rid<-rotate3d( id , -pi/2, 1, 0, 0 )
  rid2<-rotate3d( id , pi/2, 0, 0, 1 )
  rid3<-rotate3d( id , -pi/2, 0, 0, 1 )
  rgl::par3d(userMatrix = id )
  dd<-make3ViewPNG(  rid, id, rid2,  paste('network1',sep='') )
  rgl::par3d(userMatrix = id )
# another example
mni<-getANTsRData("mni")
mni<-antsImageRead(mni)
mnit<-thresholdImage( mni, 1, max(mni) )
mnit<-iMath(mnit,"FillHoles")
mniseg = kmeansSegmentation( mni, 3 )$segmentation
wmbkgd = thresholdImage( mniseg, 3, 3 ) %>% iMath( "GetLargestComponent" ) %>% iMath( "FillHoles" )
wmbkgd = smoothImage( iMath( wmbkgd, "MD", 1 ), 2.0 )
brain<-renderSurfaceFunction( surfimg =list( wmbkgd ) , alphasurf=0.8 ,smoothsval = 1.0 )
data( powers_areal_mni_itk )
coords = powers_areal_mni_itk[,1:3]
id<-rgl::par3d('userMatrix')
rid<-rotate3d( id , -pi/2, 1, 0, 0 )
rid2<-rotate3d( id , pi/2, 0, 0, 1 )
rid3<-rotate3d( id , -pi/2, 0, 0, 1 )
rgl::par3d(userMatrix = id )
handMat2 = t( matrix(  c(-0.9998656511 , 0.01626961,  0.00198165 ,   0 ,-0.0163816363, -0.99584705 ,-0.08955579   , 0, 0.0005163439, -0.08957647,  0.99597979 ,   0,  0.0000000000,  0.00000000,  0.00000000  ,  1),  ncol = 4) )
loccolor = as.character( powers_areal_mni_itk$Color )
loccolor[ loccolor == "Peach" ] = "sienna1"
loccolor[ loccolor == "Cyan" ] = "cyan"
loccolor[ loccolor == "Orange" ] = "orange"
loccolor[ loccolor == "Purple" ] = "darkorchid1"
loccolor[ loccolor == "Pink" ] = "deeppink"
loccolor[ loccolor == "Red" ] = "red"
loccolor[ loccolor == "Gray" ] = "gray74"
loccolor[ loccolor == "Teal" ] = "turquoise4"
loccolor[ loccolor == "Blue" ] = "blue"
loccolor[ loccolor == "Yellow" ] = "yellow"
loccolor[ loccolor == "Black" ] = "black"
loccolor[ loccolor == "Brown" ] = "brown"
loccolor[ loccolor == "Pale blue" ] = "steelblue1"
loccolor[ loccolor == "Green" ] = "green"
tt = plotBasicNetwork( centroids = coords, brain, nodecolors = loccolor, radius=3 )
dd<-make3ViewPNG(  handMat2, id, rid2, tempfile( fileext='.png' ) )
rgl::par3d(userMatrix = id )
# }
# NOT RUN {
# }