% \VignetteIndexEntry{Some interesting graphics}
% \VignetteDepends{circlize}
% \VignetteKeywords{circos R}
% \VignetteKeywords{circlize}
% \VignettePackage{circlize}
%\VignetteCompiler{knitr}
%\VignetteEngine{knitr::knitr}


<<echo = FALSE>>=
library(knitr)
opts_chunk$set(fig.pos = "", fig.align = "center")

library(circlize)
circos.initialize = function(...) {
    circos.par(unit.circle.segments = 300)
    circlize::circos.initialize(...)
}
@

\documentclass{article}

\usepackage[T1]{fontenc}
\usepackage[sc]{mathpazo}
\renewcommand{\sfdefault}{lmss}
\renewcommand{\ttdefault}{lmtt}

\title{Some interesting graphics}

\author{Zuguang Gu {\tt <z.gu@dkfz.de>}}
\usepackage[margin=1in, a4paper]{geometry}

\usepackage{hyperref}
\begin{document}

\maketitle 

The first example is a clock. The key function here is {\tt circos.axis} (figure \ref{fig:interesting_clock}).
The whole circle only contains one sector in which major tick at 0 is overlapping with major tick at 12.
The two arrows are plotted in the canvas coordinate. An example of a real-time clock is in {\it Examples} section in
the help page of {\tt circos.axis}.

<<interesting_clock, fig.align = "center", out.width = "0.6\\textwidth", fig.cap = "A clock.">>=
library(circlize)
factors = "a"  # any name is OK
circos.par(gap.degree = 0, cell.padding = c(0, 0, 0, 0), start.degree = 90)
circos.initialize(factors = factors, xlim = c(0, 12))
circos.trackPlotRegion(factors = factors, ylim = c(0, 1), bg.border = NA)
circos.axis(sector.index = "a", major.at = 0:12, labels = "",
    direction = "inside", major.tick.percentage = 0.3)
circos.text(1:12, rep(0.5, 12), 1:12, facing = "downward")
arrows(0, 0, 0, 0.7)    
arrows(0, 0, 0.4, 0)

circos.clear()
@


The second example is a dartboard. In the figure, tracks are assigned with different heights and each cell is initialized with
different colors (figure \ref{fig:interesting_dartboard}). The most inside green ring and red circle are plotted by {\tt draw.sector}.

<<interesting_dartboard, fig.align = "center", out.width = "0.6\\textwidth", fig.cap = "A dartboard.">>=
factors = 1:20  # just indicate there are 20 sectors
circos.par(gap.degree = 0, cell.padding = c(0, 0, 0, 0),
    start.degree = 360/20/2, track.margin = c(0, 0), clock.wise = FALSE)
circos.initialize(factors = factors, xlim = c(0, 1))
circos.trackPlotRegion(ylim = c(0, 1), factors = factors, bg.col = "black",
    track.height = 0.15)
circos.trackText(rep(0.5, 20), rep(0.5, 20),
    labels = c(13, 4, 18, 1, 20, 5, 12, 9, 14, 11, 8, 16, 7, 19, 3, 17, 2, 15, 10, 6),
    factors = factors, col = "#EEEEEE", font = 2, facing = "downward")
circos.trackPlotRegion(ylim = c(0, 1), factors = factors,
    bg.col = rep(c("#E41A1C", "#4DAF4A"), 10), bg.border = "#EEEEEE", track.height = 0.05)
circos.trackPlotRegion(ylim = c(0, 1), factors = factors,
    bg.col = rep(c("black", "white"), 10), bg.border = "#EEEEEE", track.height = 0.275)
circos.trackPlotRegion(ylim = c(0, 1), factors = factors,
    bg.col = rep(c("#E41A1C", "#4DAF4A"), 10), bg.border = "#EEEEEE", track.height = 0.05)
circos.trackPlotRegion(ylim = c(0, 1), factors = factors, 
    bg.col = rep(c("black", "white"), 10), bg.border = "#EEEEEE", track.height = 0.375)
draw.sector(center = c(0, 0), start.degree = 0, end.degree = 360,
    rou1 = 0.1, col = "#4DAF4A", border = "#EEEEEE")
draw.sector(center = c(0, 0), start.degree = 0, end.degree = 360,
    rou1 = 0.05, col = "#E41A1C", border = "#EEEEEE")

circos.clear()
@


The third example is Bagua (\url{https://en.wikipedia.org/wiki/Bagua}). The
key functions are {\tt circos.rect} and {\tt draw.sector} (figure \ref{fig:interesting_bagua}). 

Bagua is originated several thousands years ago in China. It is the source of almost all ancient
Chinese philosophy. It abstracts the rule of universe into base signs and combination of the two basic signs 
generates the whole system of the universe.

Inside Bagua, these is the Taiji (\url{http://en.wikipedia.org/wiki/Taiji_(philosophy)}). 
Taiji refers to the most original state at the creation
of the universe. In ancient Chinese philosophy system, at the very beginning, the whole world
is a huge mass of air (chaos). Then the lighter air floated up and created sky while heavier sinked down
and created ground. The upper world is called Yang and the bottom world is called Ying.
And that is Taiji.

So look at Taiji, you can see there are two states interacting with each other. The
white one and the black one gradually transformed into each other at the end. And in the center
of white and black, the opposite color is generated. In real world,
Taiji can represent all phenomenon that is of dualism. Such as male and female, correct and
wrong. However things would change, good thing would become bad thing as time goes by, and bad
thing would also turn into good according to how you look at the world.

<<interesting_bagua, fig.align = "center", out.width = "0.6\\textwidth", fig.cap = "Bagua and Taiji.">>=
factors = 1:8
circos.par(start.degree = 22.5, gap.degree = 6)
circos.initialize(factors = factors, xlim = c(0, 1))

# yang yao is -
add_yang_yao = function() {
    circos.rect(0,0,1,1, col = "black")
}

# yin yao is --
add_yin_yao = function() {
    circos.rect(0,0,0.45,1, col = "black")
    circos.rect(0.55,0,1,1, col = "black")
}
circos.trackPlotRegion(ylim = c(0, 1), factors = factors, bg.border = NA,
    panel.fun = function(x, y) {
        i = get.cell.meta.data("sector.numeric.index")
        if(i %in% c(2, 5, 7, 8)) add_yang_yao() else add_yin_yao()
}, track.height = 0.1)

circos.trackPlotRegion(ylim = c(0, 1), factors = factors, bg.border = NA,
    panel.fun = function(x, y) {
        i = get.cell.meta.data("sector.numeric.index")
        if(i %in% c(1, 6, 7, 8)) add_yang_yao() else add_yin_yao()
    }, track.height = 0.1)

circos.trackPlotRegion(ylim = c(0, 1), factors = factors, bg.border = NA, 
    panel.fun = function(x, y) {
        i = get.cell.meta.data("sector.numeric.index")
        if(i %in% c(4, 5, 6, 7)) add_yang_yao() else add_yin_yao()
    }, track.height = 0.1)

# the bottom of the most recent track
r = get.cell.meta.data("cell.bottom.radius") - 0.1
# draw taiji, note default order is clock wise for `draw.sector`
draw.sector(center = c(0, 0), start.degree = 90, end.degree = -90,
    rou1 = r, col = "black", border = "black")
draw.sector(center = c(0, 0), start.degree = 270, end.degree = 90,
    rou1 = r, col = "white", border = "black")
draw.sector(center = c(0, r/2), start.degree = 0, end.degree = 360,
    rou1 = r/2, col = "white", border = "white")
draw.sector(center = c(0, -r/2), start.degree = 0, end.degree = 360,
    rou1 = r/2, col = "black", border = "black")
draw.sector(center = c(0, r/2), start.degree = 0, end.degree = 360,
    rou1 = r/8, col = "black", border = "black")
draw.sector(center = c(0, -r/2), start.degree = 0, end.degree = 360,
    rou1 = r/8, col = "white", border = "white")

circos.clear()
@


Figure \ref{fig:painting} is a circular style of Keith Haring's doodle. 
The circular transformation is as follows: 1. use {\bf jpeg} package to read RGB
information for each pixel in the original figure; 2. use {\tt circos.rect} to draw
every pixel into the circle. Source code for generating the figure can be found
at \url{http://jokergoo.github.io/circlize/example/doodle.html}.

\begin{figure}
\centering
\includegraphics[width=0.8\textwidth]{figures/doodle.jpeg}
\caption{Keith Haring's Doodle.}
\label{fig:painting}
\end{figure}


\end{document}
