# Chord diagram, Angular mapping and Parallel coordinates VISualization

library(circlize) 

# normalize data in [0,1] interval? 0 or 1
normalize<- 0

# Read data ----
d1 <- read.csv("dec.csv", header = FALSE)
npop_d1 <- nrow(d1) # population size
nobj_d1 <- ncol(d1) # dimension
na_d1 <- matrix(data = NA, nrow = npop_d1, ncol = 3)
colnames(na_d1) <- c('rho', 'angle', 'axis')

# Transformations ----
# normalization the data on [0,1] interval

if (normalize == 1) {
  apply(d1, 2, max) -> colmax
  apply(d1, 2, min) -> colmin
  for (i in 1:npop_d1) {
    d1[i,] <- (d1[i,] - colmin) / (colmax - colmin)
  }
}

# calculate the norm, smallest angle and do the association
for (i in 1:npop_d1) {
  na_d1[i, "rho"] <- norm(d1[i,], type = "2")
  aux <- acos(d1[i,] / na_d1[i, "rho"])
  na_d1[i, "angle"] <- min(aux)
  na_d1[i, "axis"] <- which.min(aux)
}

na_d1 <- as.data.frame(na_d1)
df_d1 = data.frame(factors = na_d1$axis,
                   x = na_d1$angle,
                   y = na_d1$rho)

# Norm Angle ----
circos.clear()
circos.par(points.overflow.warning = FALSE)
circos.par(gap.after = c(rep(2, nobj_d1 - 1), 15), start.degree = 90)
#circos.initialize(factors = 1:nobj_d1, xlim = c(0, acos(1 / sqrt(nobj))))
circos.initialize(factors = 1:nobj_d1, xlim = c(min(na_d1$angle), max(na_d1$angle)))
circos.trackPlotRegion(
  factors = 1:nobj_d1,
  ylim = c(0, nobj_d1),
  track.height = 0.1,
  bg.border = NA,
  panel.fun = function(x, y) {
    circos.text(
      CELL_META$xcenter,
      CELL_META$cell.ylim[2],
      get.cell.meta.data("sector.index"),
      facing = "downward"
    )
  }
)
circos.trackPlotRegion(
  factors = 1:nobj_d1,
  ylim = c(min(c(na_d1$rho)), max(c(na_d1$rho))),
  panel.fun = function(x, y) {
    xlim = get.cell.meta.data("xlim")
    ylim = get.cell.meta.data("ylim")
    sector.index = get.cell.meta.data("sector.index")
    circos.axis(labels.cex = 0.6)
  }
)
circos.yaxis(side = "left",
             sector.index = 1,
             labels.cex = 0.6)

circos.trackPoints(na_d1$axis,
                   na_d1$angle,
                   na_d1$rho,
                   col = "blue",
                   pch = 16,
                   cex = 0.5)

# Parallel coordinates ----
circos.clear()
par(new = TRUE)
circos.par("track.height" = 0.22)
circos.par("canvas.xlim" = c(-1.5, 1.5),"canvas.ylim" = c(-1.5, 1.5))
circos.par(gap.after = c(rep(2, nobj_d1 - 1), 15), start.degree = 90)
circos.initialize(factors = 1:nobj_d1,x = 1:nobj_d1,xlim = c(1, nobj_d1))
circos.trackPlotRegion(factors = 1:nobj_d1,
                       x = 1:nobj_d1,
                       ylim = c(min(d1), max(d1)),
                       track.margin = c(0.01,0.1)
                       )
for (i in 1:nobj_d1) {
  track.margin = c(0,0.5)
  circos.xaxis(
    h = "top",
    sector.index = i,
    major.at = 1:nobj_d1,
    minor.tick = 0,
    labels.cex = 0.6
  )
}

for (i in 1:npop_d1) {
  circos.lines(
    1:nobj_d1,
    as.numeric(d1[i, ]),
    lwd = 0.2,
    sector.index = na_d1$axis[i],
    col = "blue"
  )
}
circos.yaxis(side = "left",
             sector.index = 1,
             labels.cex = 0.6)

#  Chord Diagram ----
circos.clear()
circos.par(gap.after = c(rep(2, nobj_d1 - 1), 15), start.degree = 90,track.height = 0.15)
par(new = TRUE) # <- magic
a<-2.3
circos.par("canvas.xlim" = c(-a, a),"canvas.ylim" = c(-a, a))
circos.initialize(factors = rep(1:nobj_d1, length.out = npop_d1),xlim = c(0, 1))
circos.track(
  ylim = c(0, 1),
  bg.border=c(0,0,0,0),
  panel.fun = function(x, y) {
    circos.axis(labels.cex = 0.5,
                h = "bottom",
                lwd = 1)
  }
)
for (i in 1:npop_d1) {
  for (j in 1:(nobj_d1 - 1)) {
    for (k in (j + 1):nobj_d1) {
      circos.link(j,
                  as.numeric(d1[i, j]),
                  k,
                  as.numeric((d1[i, k])),
                  col = "blue",
                  lwd = 0.2)
    }
  }
}