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mully_visualization.R
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mully_visualization.R
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getLayout <- function(g, layout) {
if (layout == "random")
return(getRandomLayout(g))
if (layout == "scaled")
return(getScaledLayout(g))
return(NULL)
}
getRandomLayout <- function(g) {
y = as.vector(V(g)$n)
g2 = g
for (i in 1:getLayersCount(g2)) {
layer = getLayerByID(g, i)
if (is.null(layer) || is.na(layer))
next
repeat {
xs = runif(length(as.vector(layer)), -4, 4)
if (!TRUE %in% duplicated(xs)) {
V(g2)[which(V(g)$n == i)]$x = xs
break
}
}
}
return(cbind(V(g2)$x, y))
}
getScaledLayout <- function(g) {
y = as.vector(V(g)$n)
g2 = g
for (i in 1:getLayersCount(g2)) {
layer = getLayerByID(g, i)
if (is.null(layer) || is.na(layer))
next
xs = (1:length(layer)) * 8 / length(layer)
V(g2)[which(V(g)$n == i)]$x = xs
}
return(cbind(V(g2)$x, y))
}
getMarkGroups <- function(g) {
l = list()
for (i in 1:g$iLayer) {
li = list(which(V(g)$n == i))
l = append(l, li)
}
return(l)
}
#' Plot the graph in 2D
#'
#' @param x The input graph
#' @param layout The layout. Can either be random or scaled
#' @param ... Other arguments to be passed to \link[igraph]{plot.igraph}
#' @return No return value. A 2D plot of the given graph is created.
#' @export
#' @import igraph
#' @importFrom randomcoloR randomColor
#' @importFrom stats runif
#' @importFrom graphics plot.new
#' @examples
#' g=mully::demo()
#' plot(g,"Scaled")
plot.mully <- function(x, layout,...) {
gps = getMarkGroups(x)
colrs = randomColor(count = x$iLayer)
assignedColors=V(x)$color
usedCols = unique(assignedColors)
if (is.null(V(x)$color))
V(x)$color = NA
for (i in 1:dim(x$layers)[1]) {
idLayer=as.integer(x$layers$ID[i])
nodesid=which(V(x)$n == idLayer)
if(is.null(nodesid) || length(nodesid)==0)
next
if (NA%in%V(x)[nodesid]$color) {
if (!colrs[idLayer] %in% usedCols) {
V(x)[nodesid]$color = colrs[idLayer]
usedCols = c(usedCols, colrs[idLayer])
}
else{
c = randomColor(count = 1)
while (c %in% usedCols) {
c = randomColor(count = 1)
}
usedCols = c(usedCols, c)
V(x)[nodesid]$color = c
}
}
}
plot.new()
# filledrectangle(wx = 1, wy = 0.5, col = "gray",mid = c(0, 0), angle = 0)
plot.igraph(x,
vertex.color = V(x)$color,
layout = getLayout(x, layout))
}
#Create 3d coordinates of the network layout on a circle
#Function copied from: https://www.blopig.com/blog/2016/10/plotting-and-storing-a-3d-network-in-r/
circpos = function(n, r = 1) {
if(n==1){
x=cos(runif(1,0, r)*r)
z=sin(runif(1,0, r)*r)
return(cbind(x,z))
}
#Coordinates on a circle
rad = seq(0, 2 * pi, length.out = n + 1)[-1]
x = cos(rad) * r
z = sin(rad) * r
return(cbind(x, z))
}
#Create 3d coordinates of the network layout on a circle
#Function inspired by: https://www.blopig.com/blog/2016/10/plotting-and-storing-a-3d-network-in-r/
discpos = function(n, r = 1) {
if(n==1){
x=cos(runif(1,0, r)*r)
z=sin(runif(1,0, r)*r)
return(cbind(x,z))
}
#Coordinates on a circle
rad = seq(0, 2 * pi, length.out = n + 1)[-1]
rad1 = runif(n+1,0, r)[-1]
x = cos(rad) * rad1
z = sin(rad) * rad1
return(cbind(x, z))
}
#' Plot the graph in 3D using rgl
#'
#' @param g The input graph
#' @param layers A boolean whether to add the layers or not
#' @param vertex.label The vertices' labels
#' @param vertex.label.color The vertices' colors. If not specified, the colors will be chosen randomly
#' @param vertex.plac The placement form of the vertices on the layer. Can either be "circle" which will place them on a circle, or "disc" which will place them randomly on a disc. The default is "circle"
#' @param edge.color The edges' colors. If not specified, inter-edges are black, and intra-edges have the same color as the nodes on the layer
#' @param edge.width The edge width. Default set to 5.
#' @param edge.arrow.size The edges' arrow size. Default set to 10
#' @param edge.arrow.width The edges' arrow width. Default set to 1
#' @return No return value. A 3D plot of the given graph is created.
#'
#'
#' @export
#' @import igraph
#' @import rgl
#' @importFrom randomcoloR randomColor
#' @importFrom stats runif
#' @note
#' This function can take the following arguments supported and not ignored by \link[igraph]{rglplot}:
#' vertex.label, vertex.label.color, edge.color, edge.width, edge.arrow.size,edge.arrow.width.
#' @examples
#' g=mully::demo()
#' labels=getNodeAttributes(g)$name
#' plot3d(g, layers=TRUE, vertex.label=labels,edge.width=6)
plot3d <- function(g, layers = TRUE,
vertex.label=NA,vertex.label.color = NA,vertex.plac="circle",
edge.color=NA,edge.width=5,
edge.arrow.size=10,edge.arrow.width=1) {
#Check if Graph is Empty
if(dim(g$layers)[1]==0){
stop("This mully Graph is empty.")
}
#Check if Graph has no nodes
if(length(V(g))==0){
stop("This mully Graph has no nodes.")
}
rgl::open3d()
rgl::bg3d(
sphere = TRUE,
color = c("white", "blue"),
lit = FALSE,
back = "lines"
)
gps = getMarkGroups(g)
nLayers=dim(g$layers)[1]
colrs = randomColor(count = g$iLayer)
assignedColors=V(g)$color
usedCols = unique(assignedColors)
if (is.null(V(g)$color))
V(g)$color = NA
for (i in 1:nLayers) {
idLayer=as.integer(g$layers$ID[i])
nodesid=which(V(g)$n == idLayer)
if(is.null(nodesid) || length(nodesid)==0)
next
if (NA%in%V(g)[nodesid]$color) {
if (!colrs[idLayer] %in% usedCols) {
V(g)[nodesid]$color = colrs[idLayer]
usedCols = c(usedCols, colrs[idLayer])
}
else{
c = randomColor(count = 1)
while (c %in% usedCols) {
c = randomColor(count = 1)
}
usedCols = c(usedCols, c)
V(g)[nodesid]$color = c
}
}
}
#List of Assigned Colors
clrs = unique(V(g)$color[order(V(g)$n)])
#Check redundant colors
indexesAC=which(clrs%in%assignedColors)
if(length(assignedColors)!=0 && length(indexesAC)!=0)
clrs=clrs[-which(clrs%in%assignedColors)]
#Add colors to the layers
g$layers$color=clrs[as.numeric(g$layers$ID)]
#Re-add assigned colors
originalColors=assignedColors[which(!is.na(assignedColors))]
if(length(originalColors)!=0)
V(g)[which(!is.na(assignedColors))]$color=originalColors
edgecolors=NULL
if(length(E(g))!=0){
#Add edge colors
if (is.null(E(g)$color))
E(g)$color = NA
if(is.na(edge.color)){
edgecolors = c()
AllEdges = getEdgeAttributes(g)
for (i in 1:dim(AllEdges)[1]) {
#Pre-assigned color
if(!is.na(E(g)$color[i]))
edgecolors=c(edgecolors,E(g)$color[i])
V1 = V(g)[which(V(g)$name == AllEdges[i, 1])]
V2 = V(g)[which(V(g)$name == AllEdges[i, 2])]
if (V1$n == V2$n)
edgecolors = c(edgecolors, clrs[which(g$layers==V1$n)])
else
edgecolors = c(edgecolors, "black")
}
edge.color=edgecolors
}
}
layout = get3DLayout(g,vertex.plac)
open3d()
igraph::rglplot(
g,
vertex.color = V(g)$color,
layout = layout,
rescale = FALSE,
vertex.label=vertex.label,
vertex.label.color = V(g)$color,
vertex.label.dist = 0,
edge.color=edgecolors,
edge.width=edge.width,
edge.arrow.size=edge.arrow.size,
edge.arrow.width=edge.arrow.width,
grouplist = unlist(gps)
)
rgl::aspect3d(1, 1, 1)
#Add layers
if (layers == TRUE) {
layout1=as.matrix(layout)
if(dim(layout1)[1]>1){
layout1 = layout[order(V(g)$n), ]
}
temp = 1
iColr=1
for (i in 1:dim(g$layers)[1]) {
idLayer=as.integer(g$layers$ID[i])
nameLayer=g$layers$Name[i]
nNodes = length(which(V(g)$n == idLayer))
if(nNodes==0)
next
if(nNodes==1)
coord = t(as.matrix(layout1[temp, ]))
else
coord = as.matrix(layout1[temp:(temp + nNodes - 1), ])
plane = get3DPlane(coord, nLayers,nNodes)
planes3d(
0,
b = plane[2],
0,
d = plane[4],
col = g$layers$color[i],
alpha = 0.2
)
#Add layers' names
rgl::text3d(
x = -max(abs(layout[, 1]))-1,
y = coord[1, 2],
z = min(abs(layout[, 3])) - 2,
texts = paste0(nameLayer," Layer",sep=""),
color = clrs[iColr],
)
iColr=iColr+1
temp = temp + nNodes
}
}
}
get3DLayout <- function(g,plac) {
yinit = 4
layers = getMarkGroups(g)
layout = list()
for (i in 1:length(layers)) {
nodesID = unlist(layers[i])
nodesInLayerCount = length(nodesID)
#layer deleted or layer empty
if(length(nodesID)==0 || nodesInLayerCount==0)
next
xz= circpos(nodesInLayerCount, r = length(layers))
if(plac=="disc")
xz = discpos(nodesInLayerCount, r = length(layers))
x = xz[, 1]
z = xz[, 2]
y = runif(n = length(nodesInLayerCount), yinit, yinit + 2)
xyz = cbind(x, y)
xyz = cbind(xyz, z)
xyz = cbind(nodesID, xyz)
layout = rbind(layout, xyz)
yinit = yinit - 4
}
dfLayout = as.data.frame(layout)
dfLayout = dfLayout[order(unlist(dfLayout$nodesID)), ]
return(cbind(
x = unlist(dfLayout$x),
y = unlist(dfLayout$y),
z = unlist(dfLayout$z)
))
}
getEquationPlane <- function(x1, y1, z1, x2, y2, z2, x3, y3, z3){
a1 = x2 - x1
b1 = y2 - y1
c1 = z2 - z1
a2 = x3 - x1
b2 = y3 - y1
c2 = z3 - z1
a = (b1 * c2) - (b2 * c1)
b = (a2 * c1) - (a1 * c2)
c = (a1 * b2) - (b1 * a2)
d = (-(a * x1) - (b * y1) - (c * z1))
return(c(a, b, c, d))
}
get3DPlane <- function(coord, iLayer,nNodes) {
p = circpos(3 + nNodes, iLayer)
temp = cbind(p[dim(p)[1] - 1:dim(p)[1], 1], rep(coord[1, 2], 3+nNodes), p[dim(p)[1] -
1:dim(p)[1], 2])
coord = rbind(coord, temp)
plane = getEquationPlane(coord[1, 1],
coord[1, 2],
coord[1, 3],
coord[2, 1],
coord[2, 2],
coord[2, 3],
coord[3, 1],
coord[3, 2],
coord[3, 3])
return(plane)
}