### 2. Zenplots ################################################################

library("zenplots")
data("olive", package = "zenplots")
zenplot(olive)

zenplot(olive, plot1d = "layout", plot2d = "layout")

str(zenplot)


### 2.1. Layout ################################################################

## Zigzagging layout methods
olive2 <- cbind(olive, olive)

zenplot(olive2, n2dcols = 6, plot1d = "layout", plot2d = "layout",
        method = "single.zigzag")
zenplot(olive2, n2dcols = 6, plot1d = "layout", plot2d = "layout",
        method = "double.zigzag")
zenplot(olive2, n2dcols = 6, plot1d = "layout", plot2d = "layout",
        method = "tidy")

## Spacings between 1d or 2d plots and around whole zenplots
zenplot(olive, plot1d = "layout", plot2d = "layout",
        method = "double.zigzag", last1d = FALSE, ispace = 0.1)
zenplot(olive, plot1d = "layout", plot2d = "layout", n2dcol = 4,
        n2dplots = 8, width1d = 2, width2d = 4)


### 3. Zenpaths ################################################################

(path <- 1:5)

zenpath(5)

# zenplot(x = dataMat[, path]) # dataMat() is a hypothetical object (does not exist; see paper)

str(zenpath)

zenpath(5, method = "front.loaded")

zenpath(5, method = "back.loaded")

zenpath(5, method = "balanced")

zenpath(c(3,5), method = "eulerian.cross")

oliveAcids <- olive[, !names(olive) %in% c("area", "region")]
zpath <- zenpath(ncol(oliveAcids))
zenplot(oliveAcids[, zpath], plot1d = "hist", plot2d = "density")


### 4. Build your own zenplots #################################################

### 4.1. Custom plot functions #################################################

zenplot(oliveAcids, plot1d = "hist", plot2d = "density", pkg = "graphics")

zenplot(oliveAcids, plot1d = hist_1d_graphics, plot2d = density_2d_graphics,
        pkg = "graphics")


### 4.3. Custom layout and plots -- a spiral of ggplots example ################

path <- c(1,2,3,1,4,2,5,1,6,2,7,1,8,2,3,4,5,3,6,4,7,3,8,4,5,6,7,5,8,6,7,8)
turns <- c("l",
           "d","d","r","r","d","d","r","r","u","u","r","r","u","u","r","r",
           "u","u","l","l","u","u","l","l","u","u","l","l","d","d","l","l",
           "u","u","l","l","d","d","l","l","d","d","l","l","d","d","r","r",
           "d","d","r","r","d","d","r","r","d","d","r","r","d","d")

library("ggplot2")
stopifnot(packageVersion("ggplot2") >= "2.2.1")
ggplot2d <- function(zargs) {
  r <- extract_2d(zargs)
  num2d <- zargs$num/2
  df <- data.frame(x = unlist(r$x), y = unlist(r$y))
  p <- ggplot() +
    geom_point(data = df, aes(x = x, y = y), cex = 0.1) +
    theme(axis.line = element_blank(),
          axis.ticks = element_blank(),
          axis.text.x = element_blank(),
          axis.text.y = element_blank(),
          axis.title.x = element_blank(),
          axis.title.y = element_blank())
  if (num2d == 1) p <- p +
    theme(panel.background = element_rect(fill = 'royalblue3'))
  if (num2d == (length(zargs$turns)-1)/2) p <- p +
    theme(panel.background = element_rect(fill = 'maroon3'))
  ggplot_gtable(ggplot_build(p))
}

zenplot(oliveAcids[,path], turns = turns, pkg = "grid",
        plot2d = function(zargs) ggplot2d(zargs))


### 4.4. Data groups ###########################################################

oliveAcids.by.area <- split(oliveAcids, f = olive$area)
names(oliveAcids.by.area)[3] <- gsub("\\.", " ", names(oliveAcids.by.area)[3])
names(oliveAcids.by.area)

zenplot(oliveAcids.by.area, labs = list(group = NULL))
zenplot(oliveAcids.by.area, lim = "groupwise", labs = list(sep = " - "),
        plot1d = function(zargs) label_1d_graphics(zargs, cex = 0.8),
        plot2d = function(zargs)
            points_2d_graphics(zargs, group... = list(sep = "\n - \n")))


### 4.5. Custom zenpaths #######################################################

library("scagnostics")
Y <- scagnostics(oliveAcids)
X <- Y["Convex", ]
d <- ncol(oliveAcids)
M <- matrix(, nrow = d, ncol = d)
M[upper.tri(M)] <- X
M[lower.tri(M)] <- t(M)[lower.tri(M)]
round(M, 5)

zpath <- zenpath(M, method = "strictly.weighted")
head(M[do.call(rbind, zpath)])

(ezpath <- extract_pairs(zpath, n = c(6, 0)))

library("graph")
plot(graph_pairs(ezpath))

(cezpath <- connect_pairs(ezpath))

oliveAcids.grouped <- groupData(oliveAcids, indices = cezpath)

zenplot(oliveAcids.grouped)


### 5. Advanced features #######################################################

### 5.1. The structure of a zenplot ############################################

res <- zenplot(olive, plot1d = "layout", plot2d = "layout", draw = FALSE)
str(res)

res[["path"]][["occupancy"]]

head(res[["path"]][["positions"]])


### 5.2. Tools for writing 1d and 2d plot functions ############################

## Bursting the data and extracting the current plot variables
points_2d_graphics

## Setting up the plot region and determining the plot indices
plot_region

plot_indices

## Unfolding the cube
n2dcols <- ncol(olive) - 1
stopifnot(identical(res, unfold(nfaces = n2dcols)))