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## Mode function:
Mode <- function(x) {
ux <- unique(x)
ux[which.max(tabulate(match(x, ux)))]
}
# Function to scale and rotate layouts:
LayoutScaler <- function(x, xrange=1, yrange=1)
{
if ((max(x[,1]) - min(x[,1])) == 0) x[,1] <- mean(xrange) else x[,1] <- (x[,1] - min(x[,1])) / (max(x[,1]) - min(x[,1])) * 2 - 1
if ((max(x[,2]) - min(x[,2])) == 0) x[,2] <- mean(yrange) else x[,2] <- (x[,2] - min(x[,2])) / (max(x[,2]) - min(x[,2])) * 2 - 1
x[,1] <- x[,1] * xrange
x[,2] <- x[,2] * yrange
return(x)
}
# Rotation function:
RotMat <- function(d,w2hrat=1)
{
matrix(c(cos(-d),sin(-d),-sin(-d),cos(-d)),2,2)
}
## Function to compute reingold-tilford layout using igraph:
rtLayout <- function(roots,GroupPars,Edgelist,layout,exoMan)
{
# Reverse intercepts in graph:
# revNodes <- which((GroupPars$edge == "int" | Edgelist[,2] %in% exoMan) & !Edgelist[,1] %in% roots )
# revNodes <- which((GroupPars$edge == "int" & !Edgelist[,1] %in% roots) | Edgelist[,2] %in% exoMan )
# Edgelist[revNodes,1:2] <- Edgelist[revNodes,2:1]
# Remove double headed arrows:
Edgelist <- Edgelist[GroupPars$edge != "<->",]
# Make igraph object:
Graph <- graph.edgelist(Edgelist, FALSE)
# Compute layout:
Layout <- layout.reingold.tilford(Graph,root=roots,circular = FALSE)
return(Layout)
}
## Function to mix color vector x with weight w
mixColfun <- function(x,w)
{
# x = vector of colors
# w = weights
if (missing(w)) w <- rep(1,length(x))
if (length(w)==1) w <- rep(w,length(x))
## w == 0 leads to NaN from weighted.mean()
w[w <= 0] <- 0.0000001
RGB <- col2rgb(x)
wMeans <- apply(RGB,1,weighted.mean,w=w)
return(rgb(wMeans[1],wMeans[2],wMeans[3],maxColorValue=255))
}
loopOptim <- function(x,Degrees)
{
NotinRange <- sum(sapply(Degrees,function(d)!any(c(d,d-2*pi,d+2*pi)>(x-pi/4) & c(d,d-2*pi,d+2*pi)<(x+pi/4))))
Dist2Edges <- sapply(Degrees,function(d)min(abs(x - c(d,d-2*pi,d+2*pi))))
return(NotinRange * 2 * pi * 2 + sum(sort(Dist2Edges)[1:2]))
}
# RotMat <- function(d) matrix(c(cos(-d),sin(-d),-sin(-d),cos(-d)),2,2)
mixInts <- function(vars,intMap,Layout,trim=FALSE,intAtSide=TRUE)
{
n <- length(vars)
if (intAtSide)
{
if (!trim)
{
if (n+nrow(intMap)==1)
{
sq <- 0
}
if (n+nrow(intMap) == 2)
{
sq <- c(0,0.5)
} else {
sq <- seq(-1,1,length=n+nrow(intMap))
}
} else {
if (n+nrow(intMap) == 2)
{
sq <- c(0,0.5)
} else {
sq <- seq(-1,1,length=n+nrow(intMap)+2)[-c(1,n+nrow(intMap)+2)]
}
}
cent <- median(1:n)
c <- 1
for (i in seq_along(vars))
{
if (vars[i]%in%intMap[,2])
{
if (i < cent)
{
Layout[intMap[intMap[,2]==vars[i],1],1] <- sq[c]
Layout[vars[i],1] <- sq[c+1]
c <- c+2
} else
{
Layout[intMap[intMap[,2]==vars[i],1],1] <- sq[c+1]
Layout[vars[i],1] <- sq[c]
c <- c+2
}
} else
{
Layout[vars[i],1] <- sq[c]
c <- c+1
}
}
} else {
if (!trim)
{
if (n==1)
{
sq <- 0
} else if (n == 2)
{
sq <- c(-1,1)
} else {
sq <- seq(-1,1,length=n)
}
} else {
if (n == 1)
{
sq <- 0
} else if (n == 2)
{
sq <- c(-0.5,0.5)
} else {
sq <- seq(-1,1,length=n+2)[-c(1,n+2)]
}
}
c <- 1
for (i in seq_along(vars))
{
if (vars[i]%in%intMap[,2])
{
Layout[intMap[intMap[,2]==vars[i],1],1] <- sq[c]
Layout[vars[i],1] <- sq[c]
c <- c + 1
} else
{
Layout[vars[i],1] <- sq[c]
c <- c+1
}
}
}
return(Layout)
}
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