plotBasicNetwork: Simple plotBasicNetwork function.

In stnava/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

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 = -1,
  backgroundColor = "white",
  nodecolors = "blue",
  nodetype = "s",
  edgeContrast = c(0, 1),
  quantileTransformWeights = FALSE,
  lwd = 2,
  minRadius = 0,
  maxRadius = 3,
  radius = NA,
  showOnlyConnectedNodes = TRUE
)

Arguments

centroids	input matrix of size N 3D points ( in rows ) by 3 ( in columns ), for N nodes.
brain	input rendering object which is output of renderSurfaceFunction. or a function derived from renderSurfaceFunction.
weights	edge weights, a symmetric matrix of size N. Weights should be non-negative.
edgecolors	a color(map) for edges. If a color map function, weights will be transformed to the range [0,1], which is compatible with functions returned by colorRamp.
backgroundColor	background color.
nodecolors	a color or color vector for nodes.
nodetype	sphere or other node type supported by RGL.
edgeContrast	a vector of length 2, specifying the contrast range for edge colors. Weights are normalized to the range [0,1]. The normalized weights can be rescaled with this parameter, eg c(0.05,0.95) would stretch the contrast over the middle 90% of normalized weight values.
quantileTransformWeights	quantile transform the weights.
lwd	line width for drawing edges.
minRadius	minimum node radius. Ignored if the radius is specified explicitly with radius.
maxRadius	maximum node radius. The node radius between minRadius and maxRadius is determined from the sum of the edge weights connecting the node. Ignored if the radius is specified explicitly with radius.
radius	a constant radius or vector of length nrow(centroids). If not specified, node radius is determined by the sum of edge weights connected to the node.
showOnlyConnectedNodes	boolean, if TRUE, only nodes with non-zero edge weights are plotted.

Details

If edgecolors is not specified, a heat-like color palette is used. Weights can be quantile transformed or clipped at a given quantile in order to improve contrast.

If weights are not specified, only the nodes are plotted.

Value

None

Author(s)

Avants BB, Duda JT, Cook PA

Examples

## 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")
mnit <- thresholdImage(mnit, 1, 2)
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, edgecolors = "red")
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)

## End(Not run)

stnava/ANTsR documentation built on April 16, 2024, 12:17 a.m.