galaaz 0.5.0 → 2.0.0

data/blogs/ruby_plot/ruby_plot.tex

@@ -0,0 +1,940 @@
+% Options for packages loaded elsewhere
+\PassOptionsToPackage{unicode}{hyperref}
+\PassOptionsToPackage{hyphens}{url}
+\documentclass[
+  11pt,
+]{article}
+\usepackage{xcolor}
+\usepackage[margin=1in]{geometry}
+\usepackage{amsmath,amssymb}
+\setcounter{secnumdepth}{5}
+\usepackage{iftex}
+\ifPDFTeX
+  \usepackage[T1]{fontenc}
+  \usepackage[utf8]{inputenc}
+  \usepackage{textcomp} % provide euro and other symbols
+\else % if luatex or xetex
+  \usepackage{unicode-math} % this also loads fontspec
+  \defaultfontfeatures{Scale=MatchLowercase}
+  \defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1}
+\fi
+\usepackage{lmodern}
+\ifPDFTeX\else
+  % xetex/luatex font selection
+\fi
+% Use upquote if available, for straight quotes in verbatim environments
+\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
+\IfFileExists{microtype.sty}{% use microtype if available
+  \usepackage[]{microtype}
+  \UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
+}{}
+\makeatletter
+\@ifundefined{KOMAClassName}{% if non-KOMA class
+  \IfFileExists{parskip.sty}{%
+    \usepackage{parskip}
+  }{% else
+    \setlength{\parindent}{0pt}
+    \setlength{\parskip}{6pt plus 2pt minus 1pt}}
+}{% if KOMA class
+  \KOMAoptions{parskip=half}}
+\makeatother
+\usepackage{color}
+\usepackage{fancyvrb}
+\newcommand{\VerbBar}{|}
+\newcommand{\VERB}{\Verb[commandchars=\\\{\}]}
+\DefineVerbatimEnvironment{Highlighting}{Verbatim}{commandchars=\\\{\}}
+% Add ',fontsize=\small' for more characters per line
+\usepackage{framed}
+\definecolor{shadecolor}{RGB}{248,248,248}
+\newenvironment{Shaded}{\begin{snugshade}}{\end{snugshade}}
+\newcommand{\AlertTok}[1]{\textcolor[rgb]{0.94,0.16,0.16}{#1}}
+\newcommand{\AnnotationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\AttributeTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{#1}}
+\newcommand{\BaseNTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
+\newcommand{\BuiltInTok}[1]{#1}
+\newcommand{\CharTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\CommentTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}}
+\newcommand{\CommentVarTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{#1}}
+\newcommand{\ControlFlowTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
+\newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{#1}}
+\newcommand{\DecValTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
+\newcommand{\DocumentationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\ErrorTok}[1]{\textcolor[rgb]{0.64,0.00,0.00}{\textbf{#1}}}
+\newcommand{\ExtensionTok}[1]{#1}
+\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
+\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
+\newcommand{\ImportTok}[1]{#1}
+\newcommand{\InformationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
+\newcommand{\NormalTok}[1]{#1}
+\newcommand{\OperatorTok}[1]{\textcolor[rgb]{0.81,0.36,0.00}{\textbf{#1}}}
+\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{#1}}
+\newcommand{\PreprocessorTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}}
+\newcommand{\RegionMarkerTok}[1]{#1}
+\newcommand{\SpecialCharTok}[1]{\textcolor[rgb]{0.81,0.36,0.00}{\textbf{#1}}}
+\newcommand{\SpecialStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\StringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\VariableTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
+\newcommand{\VerbatimStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\WarningTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\usepackage{graphicx}
+\makeatletter
+\newsavebox\pandoc@box
+\newcommand*\pandocbounded[1]{% scales image to fit in text height/width
+  \sbox\pandoc@box{#1}%
+  \Gscale@div\@tempa{\textheight}{\dimexpr\ht\pandoc@box+\dp\pandoc@box\relax}%
+  \Gscale@div\@tempb{\linewidth}{\wd\pandoc@box}%
+  \ifdim\@tempb\p@<\@tempa\p@\let\@tempa\@tempb\fi% select the smaller of both
+  \ifdim\@tempa\p@<\p@\scalebox{\@tempa}{\usebox\pandoc@box}%
+  \else\usebox{\pandoc@box}%
+  \fi%
+}
+% Set default figure placement to htbp
+\def\fps@figure{htbp}
+\makeatother
+\setlength{\emergencystretch}{3em} % prevent overfull lines
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+% usar portugues do Brasil
+% \usepackage[brazilian]{babel}
+\usepackage[utf8]{inputenc}
+
+\usepackage{geometry}
+\geometry{a4paper, top=1in}
+
+% needed for kableExtra
+\usepackage{longtable}
+\usepackage{multirow}
+\usepackage[table]{xcolor}
+\usepackage{wrapfig}
+\usepackage{float}
+\usepackage{colortbl}
+\usepackage{pdflscape}
+\usepackage{tabu}
+\usepackage{threeparttable}
+\usepackage[normalem]{ulem}
+
+\usepackage{bbm}
+\usepackage{booktabs}
+\usepackage{expex}
+
+\usepackage{graphicx}
+
+\usepackage{fancyhdr}
+% set the header and foot style
+% style 'fancy' adds the section name on the header
+% and the page number on the footer
+\pagestyle{fancy}
+
+% style 'fancyhf' leaves header and footer empty
+%\fancyhf{}
+
+% sets the left head element to \rightmark, which contains the
+% current section (\leftmark is the current chapter)
+%\fancyhead[L]{\rightmark} .
+
+% sets the right head element to the page number.
+% \fancyhead[R]{\thepage}
+
+% lets the head rule disappear.
+% \renewcommand{\headrulewidth}{0pt}
+% Possible selectors for the optional argument of \fancyhead/\fancyfoot
+% are L (left), C (center) or R (right) for the position of the element
+% and E (even) or O (odd) to distinguish even and odd pages. If you omit
+% E/O the element is set for all pages.
+
+% \usepackage{lipsum}
+
+% make available command lastpage
+\usepackage{lastpage}
+
+% default fontsize 11pt better to add
+% fontsize on the yaml header
+% \usepackage[fontsize=11pt]{scrextend}
+
+% comandos para formatar uma tabela
+\usepackage{array}
+\newcolumntype{L}[1]{>{\raggedright\let\newline\\\arraybackslash\hspace{0pt}}m{#1}}
+\newcolumntype{C}[1]{>{\centering\let\newline\\\arraybackslash\hspace{0pt}}m{#1}}
+\newcolumntype{R}[1]{>{\raggedleft\let\newline\\\arraybackslash\hspace{0pt}}m{#1}}
+
+% necessário if we need to import other latex documents
+\usepackage{import}
+
+% Command to import an R variable to latex
+\newcommand{\RtoLatex}[2]{\newcommand{#1}{#2}}
+
+% 
+%\newcommand{\atraso}[1]{\color{red} \textbf {Tempo desde a Assinatura do Contrato: #1 dias}}
+\usepackage{bookmark}
+\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
+\urlstyle{same}
+\hypersetup{
+  pdftitle={How to make Beautiful Ruby Plots with Galaaz},
+  pdfauthor={Rodrigo Botafogo; Daniel Mossé - University of Pittsburgh},
+  hidelinks,
+  pdfcreator={LaTeX via pandoc}}
+
+\title{How to make Beautiful Ruby Plots with Galaaz}
+\author{Rodrigo Botafogo \and Daniel Mossé - University of Pittsburgh}
+\date{November 19th, 2018 (narrative updated for Galaaz 2.0, 2026)}
+
+\begin{document}
+\maketitle
+
+{
+\setcounter{tocdepth}{2}
+\tableofcontents
+}
+According to Wikipedia ``Ruby is a dynamic, interpreted, reflective,
+object-oriented, general-purpose programming language. It was designed
+and developed in the mid-1990s by Yukihiro''Matz'' Matsumoto in Japan.''
+It reached high popularity with the development of Ruby on Rails (RoR)
+by David Heinemeier Hansson. RoR is a web application framework first
+released around 2005. It makes extensive use of Ruby's metaprogramming
+features. With RoR, Ruby became very popular. According to
+\href{https://www.tiobe.com/tiobe-index/ruby/}{Ruby's Tiobe index} it
+peeked in popularity around 2008, then declined until 2015 when it
+started picking up again. At the time of this writing (November 2018),
+the Tiobe index puts Ruby in 16th position as most popular language.
+
+Python, a language similar to Ruby, ranks 4th in the index. Java, C and
+C++ take the first three positions. Ruby is often criticized for its
+focus on web applications. But Ruby can do
+\href{https://github.com/markets/awesome-ruby}{much more} than just web
+applications. Yet, for scientific computing, Ruby lags way behind Python
+and R. Python has Django framework for web, NumPy for numerical arrays,
+Pandas for data analysis. R is a free software environment for
+statistical computing and graphics with thousands of libraries for data
+analysis.
+
+Until recently, there was no real perspective for Ruby to bridge this
+gap. Implementing a complete scientific computing infrastructure would
+take too long.
+
+\textbf{Galaaz 2.0} couples
+\textbf{\href{https://www.jruby.org/}{JRuby}} (Ruby on the JVM) with
+\textbf{GNU R}---the same R distribution used for data science
+everywhere. A \textbf{bridge} evaluates R from Ruby and exchanges data
+between the two processes so that, from Ruby, you call R functions and
+work with R objects using familiar Ruby syntax. In other words, a Ruby
+programmer can use the capabilities of R without memorizing all of R's
+syntax for day-to-day tasks.
+
+An \textbf{earlier line of work} used Oracle's \textbf{GraalVM} with
+\textbf{TruffleRuby} and \textbf{FastR} so that Ruby and R could share
+one JVM runtime. That stack is \textbf{no longer} what Galaaz targets;
+today's Galaaz is developed and tested with \textbf{JRuby + GNU R} (see
+the project manual for setup and command-line tools).
+
+Library wrapping is a usual way of bringing features from one language
+into another. To improve performance, Python often wraps more efficient
+C libraries. For the Python developer, the existence of such C libraries
+is hidden. The problem with library wrapping is that for any new
+library, there is the need to handcraft a new wrapper.
+
+Galaaz, instead of wrapping a single C or R library, wraps the whole R
+language in Ruby. Doing so, all thousands of R libraries are available
+immediately to Ruby developers without any new wrapping effort.
+
+To show the power of Galaaz, we show in this article how Ruby can use
+R's ggplot2 library tranparantly bringing to Ruby the power of high
+quality scientific plotting. We also show that migrating from R to Ruby
+with Galaaz is a matter of small syntactic changes. By using Ruby, the R
+developer can use all of Ruby's powerful object-oriented features. Also,
+with Ruby, it becomes much easier to move code from the analysis phase
+to the production phase.
+
+In this article we will explore the R ToothGrowth dataset. To
+illustrate, we will create some boxplots. A primer on boxplot is
+available in
+\href{https://towardsdatascience.com/understanding-boxplots-5e2df7bcbd51}{this
+article}.
+
+We will also create a Corporate Template ensuring that plots will have a
+consistent visualization. This template is built using a Ruby module.
+There is a way of building ggplot themes that will work the same as the
+Ruby module. Yet, writing a new theme requires specific knowledge on
+theme writing. Ruby modules are standard to the language and don't need
+special knowledge.
+
+\href{https://towardsdatascience.com/ruby-plotting-with-galaaz-an-example-of-tightly-coupling-ruby-and-r-in-graalvm-520b69e21021}{Here}
+is an older article (GraalVM-era Galaaz) with a scatter plot in Ruby;
+the \textbf{ideas} still apply under Galaaz 2.0 with JRuby and GNU R.
+
+\section{gKnit}\label{gknit}
+
+\emph{Knitr} is an application that converts text written in rmarkdown
+to many different output formats. For instance, a writer can convert an
+rmarkdown document to HTML, \(LaTex\), docx and many other formats.
+Rmarkdown documents can contain text and \emph{code chunks}. Knitr
+formats code chunks in a grayed box in the output document. It also
+executes the code chunks and formats the output in a white box. Every
+line of output from the execution code is preceded by `\#\#'.
+
+Knitr allows code chunks to be in R, Python, Ruby and dozens of other
+languages. Yet, while R and Python chunks can share data, in other
+languages, chunks are independent. This means that a variable defined in
+one chunk cannot be used in another chunk.
+
+With \emph{gKnit} Ruby code chunks can share data.
+
+\section{Exploring the Dataset}\label{exploring-the-dataset}
+
+Let's start by exploring our selected dataset. ToothGrowth is an R
+dataset. A dataset is like a simple excel spreadsheet, in which each
+column has only one type of data. For instance one column can have
+float, the other integer, and a third strings. This dataset analyzes the
+length of odontoblasts (cells responsible for tooth growth) in 60 guinea
+pigs, where each animal received one of three dose levels of Vitamin C
+(0.5, 1, and 2 mg/day) by one of two delivery methods, orange juice OJ
+or ascorbic acid (a form of vitamin C and coded as VC).
+
+The ToothGrowth dataset contains three columns: `len', `supp' and
+`dose'. Let's take a look at a few rows of this dataset. In Galaaz, R
+variables are accessed by using the corresponding Ruby symbol preceeded
+by the tilda (`\textasciitilde{}') function. Note in the following chunk
+that `ToothGrowth' is the R variable and Ruby's `tooth\_growth' is
+assigned the value of `\textasciitilde:ToothGrowth'.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\CommentTok{\# Read the R ToothGrowth variable and assign it to the}
+\CommentTok{\# Ruby instance variable tooth\_growth that will be }
+\CommentTok{\# available to all Ruby chunks in this document.}
+\NormalTok{tooth\_growth }\OperatorTok{=} \OperatorTok{\textasciitilde{}}\WarningTok{:ToothGrowth}
+\CommentTok{\# print the first few elements of the dataset}
+\FunctionTok{puts}\NormalTok{ tooth\_growth}\AttributeTok{.head}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{verbatim}
+##    len supp dose
+## 1  4.2   VC  0.5
+## 2 11.5   VC  0.5
+## 3  7.3   VC  0.5
+## 4  5.8   VC  0.5
+## 5  6.4   VC  0.5
+## 6 10.0   VC  0.5
+\end{verbatim}
+
+Great! We've managed to read the ToothGrowth dataset and take a look at
+its elements. We see here the first 6 rows of the dataset. To access a
+column, follow the dataset name with a dot (`.') and the name of the
+column. Also use dot notation to chain methods in usual Ruby style.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\CommentTok{\# Access the tooth\_growth \textquotesingle{}len\textquotesingle{} column and print the first few}
+\CommentTok{\# elements of this column with the \textquotesingle{}head\textquotesingle{} method.}
+\FunctionTok{puts}\NormalTok{ tooth\_growth}\AttributeTok{.len.head}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{verbatim}
+## [1]  4.2 11.5  7.3  5.8  6.4 10.0
+\end{verbatim}
+
+The `dose' column contains a numeric value with either, 0.5, 1 or 2,
+although the first 6 rows as seen above only contain the 0.5 values.
+Even though those are number, they are better interpreted as a
+\href{https://swcarpentry.github.io/r-novice-inflammation/12-supp-factors/}{factor
+or cathegory}. So, let's convert our `dose' column from numeric to
+`factor'. In R, the function `as.factor' is used to convert data in a
+vector to factors. To use this function from Galaaz the dot (`.') in the
+function name is substituted by '\_\_' (double underline). The function
+`as.factor' becomes 'R.as\_\_factor' or just 'as\_\_factor' when
+chaining.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\CommentTok{\# convert the dose to a factor}
+\NormalTok{tooth\_growth}\AttributeTok{.dose} \OperatorTok{=}\NormalTok{ tooth\_growth}\AttributeTok{.dose.as\_\_factor}
+\end{Highlighting}
+\end{Shaded}
+
+Let's explore some more details of this dataset. In particular, let's
+look at its dimensions, structure and summary statistics.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\FunctionTok{puts}\NormalTok{ tooth\_growth}\AttributeTok{.dim}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{verbatim}
+## [1] 60  3
+\end{verbatim}
+
+This dataset has 60 rows, one for each subject and 3 columns, as we have
+already seen.
+
+Note that we do not need to call `puts' when using the `str' function.
+This functions does not return anything and prints the structure of the
+dataset as a side effect.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\NormalTok{tooth\_growth}\AttributeTok{.str}
+\end{Highlighting}
+\end{Shaded}
+
+Observe that both variables `supp' and `dose' are factors. The system
+made variable `supp' a factor automatically, since it contais two
+strings OJ and VC.
+
+Finally, using the summary method, we get the statistical summary for
+the dataset
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\FunctionTok{puts}\NormalTok{ tooth\_growth}\AttributeTok{.summary}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{verbatim}
+##       len        supp     dose   
+##  Min.   : 4.20   OJ:30   0.5:20  
+##  1st Qu.:13.07   VC:30   1  :20  
+##  Median :19.25           2  :20  
+##  Mean   :18.81                   
+##  3rd Qu.:25.27                   
+##  Max.   :33.90
+\end{verbatim}
+
+\section{Doing the Data Analysis}\label{doing-the-data-analysis}
+
+\subsection{Quick plot for seing the
+data}\label{quick-plot-for-seing-the-data}
+
+Let's now create our first plot with the given data by accessing ggplot2
+from Ruby. For Rubyists that have never seen or used ggplot2, here is
+the description of ggplot found in its home page:
+
+\begin{quote}
+``ggplot2 is a system for declaratively creating graphics, based on
+\emph{The Grammar of Graphics}. You provide the data, tell ggplot2 how
+to map variables to aesthetics, what graphical primitives to use, and it
+takes care of the details.''
+\end{quote}
+
+This description might be a bit cryptic and it is best to see it at work
+to understand it. Basically, in the \emph{grammar of graphics}
+developers add layers of components such as grid, axis, data, title,
+subtitle and also graphical primitives such as \emph{bar plot},
+\emph{box plot}, to form the final graphics.
+
+In order to make a plot, we use the `ggplot' function to the dataset. In
+R, this would be written as
+\texttt{ggplot(\textless{}dataset\textgreater{},\ ...)}. Galaaz gives
+you the flexibility to use either
+\texttt{R.ggplot(\textless{}dataset\textgreater{},\ ...)} or
+\texttt{\textless{}dataset\textgreater{}.ggplot(...)}. In the graph
+specification bellow, we use the second notation that looks more like
+Ruby.\\
+ggplot uses the `aes' method to specify x and y axes; in this case, the
+`dose' on the \(x\) axis and the `length' on the \(y\) axis: `E.aes(x:
+:dose, y: :len)'. To specify the type of plot add a geom to the plot.
+For a boxplot, the geom is R.geom\_boxplot.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\FunctionTok{require} \VerbatimStringTok{\textquotesingle{}ggplot\textquotesingle{}}
+
+\NormalTok{e }\OperatorTok{=}\NormalTok{ tooth\_growth}\AttributeTok{.ggplot}\NormalTok{(}\ConstantTok{E}\AttributeTok{.aes}\NormalTok{(}\WarningTok{x:} \WarningTok{:dose}\NormalTok{, }\WarningTok{y:} \WarningTok{:len}\NormalTok{))}
+\FunctionTok{print}\NormalTok{ e }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.geom\_boxplot}
+\end{Highlighting}
+\end{Shaded}
+
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/dose_len.png}}
+
+Great! We've just managed to create and save our first plot in Ruby with
+only four lines of code. We can now easily see with this plot a clear
+trend: as the dose of the supplement is increased, so is the length of
+teeth.
+
+\subsection{Facetting the plot}\label{facetting-the-plot}
+
+This first plot shows a trend, but our data has information about two
+different forms of delivery method, either by Orange Juice OJ or by
+Vitamin C VC. Let's then try to create a plot that helps us discern the
+effect of each delivery method. This next plot is a \emph{facetted} plot
+where each delivery method gets is own plot. On the left side, the plot
+shows the OJ delivery method. On the right side, we see the VC delivery
+method. To obtain this plot, we use the `R.facet\_grid' function, that
+automatically creates the facets based on the delivery method factors.
+The parameter to the `facet\_grid' method is a
+\href{https://thomasleeper.com/Rcourse/Tutorials/formulae.html}{\emph{formula}}.
+
+In Galaaz we give programmers the flexibility to use two different ways
+to write formulas. In the first way, we use Ruby expressions and the
+`.til' function. The formula `x \textasciitilde{} y', becomes `:x.til
+:y'. More information on expressions can be found in
+\href{https://www.rubydoc.info/gems/galaaz/}{Galaaz Manual}.
+
+Another way of writing a formula is to use the `formula' function with
+the actual formula as a string. The formula
+\texttt{x\ \textasciitilde{}\ y} in R can be written as
+\texttt{R.formula("x\ \textasciitilde{}\ y")}. For more complex
+formulas, the use of the `formula' function is preferred.
+
+The formula \texttt{:all.til\ :supp} indicates to the `facet\_grid'
+function that it needs to facet the plot based on the \texttt{supp}
+variable and split the plot vertically. Changing the formula to
+\texttt{:supp.til\ :all} would split the plot horizontally.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\NormalTok{base\_tooth }\OperatorTok{=}\NormalTok{ tooth\_growth}\AttributeTok{.ggplot}\NormalTok{(}\ConstantTok{E}\AttributeTok{.aes}\NormalTok{(}\WarningTok{x:} \WarningTok{:dose}\NormalTok{, }\WarningTok{y:} \WarningTok{:len}\NormalTok{, }\WarningTok{group:} \WarningTok{:dose}\NormalTok{))}
+
+\NormalTok{bp }\OperatorTok{=}\NormalTok{ base\_tooth }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.geom\_boxplot} \OperatorTok{+}
+      \CommentTok{\# Split in vertical direction}
+      \ConstantTok{R}\AttributeTok{.facet\_grid}\NormalTok{(}\WarningTok{:all}\AttributeTok{.til} \OperatorTok{:}\NormalTok{supp)}
+
+\FunctionTok{puts}\NormalTok{ bp}
+\end{Highlighting}
+\end{Shaded}
+
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/facet_by_delivery.png}}
+
+It now becomes clear that although both methods of delivery have a
+direct impact on tooth growth, method (OJ) is non-linear having a higher
+impact with smaller doses of ascorbic acid and reducing it's impact as
+the dose increases. With the (VC) approach, the impact seems to be more
+linear.
+
+\subsection{Adding Color}\label{adding-color}
+
+If we were writing about data analysis, we would make a better analysis
+of the trends and improve the statistical analysis. But here we are
+interested in working with ggplot in Ruby. So, let's add some color to
+this plot to make the trend and comparison more visible. In the
+following plot, the boxes are color coded by dose. To add color, it is
+enough to add \texttt{fill:\ :dose} to the aesthetic of boxplot. With
+this command each `dose' factor gets its own color.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\NormalTok{bp }\OperatorTok{=}\NormalTok{ bp }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.geom\_boxplot}\NormalTok{(}\ConstantTok{E}\AttributeTok{.aes}\NormalTok{(}\WarningTok{fill:} \WarningTok{:dose}\NormalTok{))}
+\FunctionTok{puts}\NormalTok{ bp}
+\end{Highlighting}
+\end{Shaded}
+
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/facets_by_delivery_color.png}}
+
+Facetting helps us compare the general trends for each delivery method.
+Adding color allow us to compare specifically how each dosage impacts
+the tooth growth. It is possible to observe that with smaller doses, up
+to 1mg, OJ performs better than VC (red color). For 2mg, both OJ and VC
+have the same median, but OJ is less disperse (blue color). For 1mg
+(green color), OJ is significantly bettern than VC. By this very quick
+visual analysis, it seems that OJ is a better delivery method than VC.
+
+\subsection{Clarifying the data}\label{clarifying-the-data}
+
+Boxplots give us a nice idea of the distribution of data, but looking at
+those plots with large colored boxes leaves us wondering what else is
+going on. According to Edward Tufte in Envisioning Information:
+
+\begin{quote}
+Thin data rightly prompts suspicions: ``What are they leaving out? Is
+that really everything they know? What are they hiding? Is that all they
+did?'' Now and then it is claimed that vacant space is ``friendly''
+(anthropomorphizing an inherently murky idea) but \emph{it is not how
+much empty space there is, but rather how it is used. It is not how much
+information there is, but rather how effectively it is arranged.}
+\end{quote}
+
+And he states:
+
+\begin{quote}
+A most unconventional design strategy is revealed: \emph{to clarify, add
+detail.}
+\end{quote}
+
+Let's use this wisdom and add yet another layer of data to our plot, so
+that we clarify it with detail and do not leave large empty boxes. In
+this next plot, we add data points for each of the 60 pigs in the
+experiment. For that, add the function `R.geom\_point' to the plot.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\CommentTok{\# Split in vertical direction}
+\NormalTok{bp }\OperatorTok{=}\NormalTok{ bp }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.geom\_point}
+
+\FunctionTok{puts}\NormalTok{ bp}
+\end{Highlighting}
+\end{Shaded}
+
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/facets_with_points.png}}
+
+Now we can see the actual distribution of all the 60 subjects. Actually,
+this is not totally true. We have a hard time seing all 60 subjects. It
+seems that some points might be placed one over the other hiding useful
+information.
+
+But no sweat! Another layer might solve the problem. In the following
+plot a new layer called `geom\_jitter' is added to the plot. Jitter adds
+a small amount of random variation to the location of each point, and is
+a useful way of handling overplotting caused by discreteness in smaller
+datasets. This makes it easier to see all of the points and prevents
+data hiding. We also add color and change the shape of the points,
+making them even easier to see.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\CommentTok{\# Split in vertical direction}
+\FunctionTok{puts}\NormalTok{ bp }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.geom\_jitter}\NormalTok{(}\WarningTok{shape:} \DecValTok{23}\NormalTok{, }\WarningTok{color:} \StringTok{"cyan3"}\NormalTok{, }\WarningTok{size:} \DecValTok{1}\NormalTok{)}
+\end{Highlighting}
+\end{Shaded}
+
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/facets_with_jitter.png}}
+
+Now we can see all 60 points in the graph. We have here a much higher
+information density and we can see outliers and subjects distribution.
+
+\section{Preparing the Plot for
+Presentation}\label{preparing-the-plot-for-presentation}
+
+We have come a long way since our first plot. As we already said, this
+is not an article about data analysis and the focus is on the
+integration of Ruby and ggplot. So, let's assume that the analysis is
+now done. Yet, ending the analysis does not mean that the work is done.
+On the contrary, the hardest part is yet to come!
+
+After the analysis it is necessary to communicate it by making a final
+plot for presentation. The last plot has all the information we want to
+share, but it is not very pleasing to the eye.
+
+\subsection{Improving Colors}\label{improving-colors}
+
+Let's start by trying to improve colors. For now, we will not use the
+jitter layer. The previous plot has three bright colors that have no
+relashionship between them. Is there any obvious, or non-obvious for
+that matter, interpretation for the colors? Clearly, they are just
+random colors selected automatically by our software. Although those
+colors helped us understand the data, for a final presentation random
+colors can distract the viewer.
+
+In the following plot we use shades function `scale\_fill\_manual' to
+change the colors of the boxes and order of labels. For colors, we use
+shades of blue for each dosage, with light blue (`cyan') representing
+the lower dose and deep blue (`deepskyblue4') the higher dose. Also, the
+legend could be improved: we use the `breaks' parameter to put the
+smaller value (0.5) at the botton of the labels and the largest (2) at
+the top. This ordering seems more natural and matches with the actual
+order of the colors in the plot.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\NormalTok{bp }\OperatorTok{=}\NormalTok{ bp }\OperatorTok{+}
+     \ConstantTok{R}\AttributeTok{.scale\_fill\_manual}\NormalTok{(}\WarningTok{values:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\StringTok{"cyan"}\NormalTok{, }\StringTok{"deepskyblue"}\NormalTok{, }\StringTok{"deepskyblue4"}\NormalTok{),}
+                          \WarningTok{breaks:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\StringTok{"2"}\NormalTok{,}\StringTok{"1"}\NormalTok{,}\StringTok{"0.5"}\NormalTok{))}
+
+\FunctionTok{puts}\NormalTok{ bp}
+\end{Highlighting}
+\end{Shaded}
+
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/facets_by_delivery_color2.png}}
+
+\subsection{Violin Plot and Jitter}\label{violin-plot-and-jitter}
+
+The boxplot with jitter did look a bit overwhelming. The next plot uses
+a variation of a boxplot known as a \emph{violin plot} with jittered
+data.
+
+\href{https://en.wikipedia.org/wiki/Violin_plot}{From Wikipedia}
+
+\begin{quote}
+A violin plot is a method of plotting numeric data. It is similar to a
+box plot with a rotated kernel density plot on each side.
+
+A violin plot has four layers. The outer shape represents all possible
+results, with thickness indicating how common. (Thus the thickest
+section represents the mode average.) The next layer inside represents
+the values that occur 95\% of the time. The next layer (if it exists)
+inside represents the values that occur 50\% of the time. The central
+dot represents the median average value.
+\end{quote}
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\NormalTok{violin }\OperatorTok{=}\NormalTok{ base\_tooth }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.geom\_violin}\NormalTok{(}\ConstantTok{E}\AttributeTok{.aes}\NormalTok{(}\WarningTok{fill:} \WarningTok{:dose}\NormalTok{)) }\OperatorTok{+} 
+   \ConstantTok{R}\AttributeTok{.facet\_grid}\NormalTok{(}\WarningTok{:all}\AttributeTok{.til} \OperatorTok{:}\NormalTok{supp) }\OperatorTok{+}
+   \ConstantTok{R}\AttributeTok{.geom\_jitter}\NormalTok{(}\WarningTok{shape:} \DecValTok{23}\NormalTok{, }\WarningTok{color:} \StringTok{"cyan3"}\NormalTok{, }\WarningTok{size:} \DecValTok{1}\NormalTok{) }\OperatorTok{+}
+   \ConstantTok{R}\AttributeTok{.scale\_fill\_manual}\NormalTok{(}\WarningTok{values:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\StringTok{"cyan"}\NormalTok{, }\StringTok{"deepskyblue"}\NormalTok{, }\StringTok{"deepskyblue4"}\NormalTok{),}
+                       \WarningTok{breaks:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\StringTok{"2"}\NormalTok{,}\StringTok{"1"}\NormalTok{,}\StringTok{"0.5"}\NormalTok{))}
+
+\FunctionTok{puts}\NormalTok{ violin}
+\end{Highlighting}
+\end{Shaded}
+
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/violin_with_jitter.png}}
+
+This plot is an alternative to the original boxplot. For the final
+presentation, it is important to think which graphics will be best
+understood by our audience. A violin plot is a less known plot and could
+add mental overhead, yet, in my opinion, it does look a lit bit better
+than the boxplot and provides even more information than the boxplot
+with jitter.
+
+\subsection{Adding Decoration}\label{adding-decoration}
+
+Our final plot is starting to take shape, but a presentation plot should
+have at least a title, labels on the axes and maybe some other
+decorations. Let's start adding those. Since decoration requires more
+graph area, this new plot has a `width' and `height' specification. When
+there is no specification, the default values from R for width and
+height are 480.
+
+The `labs' function adds the required decoration. In this example we use
+`title', `subtitle', `x' for the \(x\) axis label and `y', for the \(y\)
+axis label, and `caption' for information about the plot (for clarity,
+we defined a caption variable using Ruby's Here Doc style).
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\NormalTok{caption }\OperatorTok{=} \OperatorTok{\textless{}\textless{}{-}}\ControlFlowTok{EOT}
+\DocumentationTok{Length of odontoblasts in 60 guinea pigs. }
+\DocumentationTok{Each animal received one of three dose levels of vitamin C.}
+\ControlFlowTok{EOT}
+
+\NormalTok{decorations }\OperatorTok{=}
+  \ConstantTok{R}\AttributeTok{.labs}\NormalTok{(}\WarningTok{title:} \StringTok{"Tooth Growth:  Length vs Vitamin C Dose"}\NormalTok{,}
+         \WarningTok{subtitle:} \StringTok{"Faceted by delivery method, OJ or VC"}\NormalTok{,}
+         \WarningTok{x:} \StringTok{"Dose (mg)"}\NormalTok{, }\WarningTok{y:} \StringTok{"Teeth length"}\NormalTok{,}
+         \WarningTok{caption:}\NormalTok{ caption)}
+
+\FunctionTok{puts}\NormalTok{ bp }\OperatorTok{+}\NormalTok{ decorations}
+\end{Highlighting}
+\end{Shaded}
+
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/facets_with_decorations.png}}
+
+\subsection{The Corp Theme}\label{the-corp-theme}
+
+We are almost done. But the default plot configuration does not yet look
+nice to the eye. We are still distracted by many aspects of the graph.
+First, the back font color does not look good. Then plot background,
+borders, grids all add clutter to the plot.
+
+We will now define our corporate theme. in a module that can be
+used/loaded for all plots, similar to CSS or any other style definition.
+
+In this theme, we remove borders and grids. The background if left for
+faceted plots but removed for non-faceted plots. Font colors are a shade
+o blue (color: `\#00080'). Axis labels are moved near the end of the
+axis and written in `bold'.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\ControlFlowTok{module} \DataTypeTok{CorpTheme}
+
+  \ConstantTok{R}\AttributeTok{.install\_and\_loads} \VerbatimStringTok{\textquotesingle{}RColorBrewer\textquotesingle{}}
+  
+  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
+  \CommentTok{\# face can be  (1=plain, 2=bold, 3=italic, 4=bold{-}italic)}
+  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
+  
+  \ControlFlowTok{def} \DecValTok{self}\AttributeTok{.text\_element}\NormalTok{(size, }\WarningTok{face:} \StringTok{"plain"}\NormalTok{, }\WarningTok{hjust:} \DecValTok{nil}\NormalTok{)}
+    \ConstantTok{E}\AttributeTok{.element\_text}\NormalTok{(}\WarningTok{color:} \StringTok{"\#000080"}\NormalTok{, }
+                   \WarningTok{face:}\NormalTok{ face,}
+                   \WarningTok{size:}\NormalTok{ size,}
+           \WarningTok{hjust:}\NormalTok{ hjust)}
+  \ControlFlowTok{end}
+  
+  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
+  \CommentTok{\# Defines the plot theme (visualization).  In this theme we remove major and minor}
+  \CommentTok{\# grids, borders and background.  We also turn{-}off scientific notation.}
+  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
+  
+  \ControlFlowTok{def} \DecValTok{self}\AttributeTok{.global\_theme}\NormalTok{(faceted }\OperatorTok{=} \DecValTok{false}\NormalTok{)}
+    
+    \ConstantTok{R}\AttributeTok{.options}\NormalTok{(}\WarningTok{scipen:} \DecValTok{999}\NormalTok{)  }\CommentTok{\# turn{-}off scientific notation like 1e+48}
+    \CommentTok{\#    R.theme\_set(R.theme\_bw)}
+    
+    \CommentTok{\# remove major grids}
+\NormalTok{    gb }\OperatorTok{=} \ConstantTok{R}\AttributeTok{.theme}\NormalTok{(}\WarningTok{panel\_\_grid\_\_major:} \ConstantTok{E}\AttributeTok{.element\_blank}\NormalTok{())}
+    \CommentTok{\# remove minor grids}
+\NormalTok{    gb }\OperatorTok{=}\NormalTok{ gb }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.theme}\NormalTok{(}\WarningTok{panel\_\_grid\_\_minor:} \ConstantTok{E}\AttributeTok{.element\_blank}\NormalTok{)}
+    \CommentTok{\# gb = R.theme(panel\_\_grid\_\_minor: E.element\_blank)}
+    \CommentTok{\# remove border}
+\NormalTok{    gb }\OperatorTok{=}\NormalTok{ gb }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.theme}\NormalTok{(}\WarningTok{panel\_\_border:} \ConstantTok{E}\AttributeTok{.element\_blank}\NormalTok{)}
+    \CommentTok{\# remove background. When working with faceted graphs, the background makes}
+    \CommentTok{\# it easier to see each facet, so leave it}
+\NormalTok{    gb }\OperatorTok{=}\NormalTok{ gb }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.theme}\NormalTok{(}\WarningTok{panel\_\_background:} \ConstantTok{E}\AttributeTok{.element\_blank}\NormalTok{) }\ControlFlowTok{if} \OperatorTok{!}\NormalTok{faceted}
+    \CommentTok{\# Change axis font}
+\NormalTok{    gb }\OperatorTok{=}\NormalTok{ gb }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.theme}\NormalTok{(}\WarningTok{axis\_\_text:}\NormalTok{ text\_element(}\DecValTok{8}\NormalTok{))}
+    \CommentTok{\# change axis title font}
+\NormalTok{    gb }\OperatorTok{=}\NormalTok{ gb }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.theme}\NormalTok{(}\WarningTok{axis\_\_title:}\NormalTok{ text\_element(}\DecValTok{10}\NormalTok{, }\WarningTok{face:} \StringTok{"bold"}\NormalTok{, }\WarningTok{hjust:} \DecValTok{1}\NormalTok{))}
+    \CommentTok{\# change font of title}
+\NormalTok{    gb }\OperatorTok{=}\NormalTok{ gb }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.theme}\NormalTok{(}\WarningTok{title:}\NormalTok{ text\_element(}\DecValTok{12}\NormalTok{, }\WarningTok{face:} \StringTok{"bold"}\NormalTok{))}
+    \CommentTok{\# change font of subtitle}
+\NormalTok{    gb }\OperatorTok{=}\NormalTok{ gb }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.theme}\NormalTok{(}\WarningTok{plot\_\_subtitle:}\NormalTok{ text\_element(}\DecValTok{9}\NormalTok{))}
+    \CommentTok{\# change font of captions}
+\NormalTok{    gb }\OperatorTok{=}\NormalTok{ gb }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.theme}\NormalTok{(}\WarningTok{plot\_\_caption:}\NormalTok{ text\_element(}\DecValTok{8}\NormalTok{))}
+
+  \ControlFlowTok{end}
+   
+\ControlFlowTok{end}
+\end{Highlighting}
+\end{Shaded}
+
+\subsection{Final Box Plot}\label{final-box-plot}
+
+We can now easily make our final boxplot and violin plot. All the layers
+for the plot were added in order to expose our understanding of the data
+and the need to present the result to our audience.
+
+The final specification is just the addition of all layers build up to
+this point (`bp'), plus the decorations (`decorations'), plus the
+corporate theme.
+
+Here is our final boxplot, without jitter.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\FunctionTok{puts}\NormalTok{ bp }\OperatorTok{+}\NormalTok{ decorations }\OperatorTok{+} \DataTypeTok{CorpTheme}\AttributeTok{.global\_theme}\NormalTok{(}\WarningTok{faceted:} \DecValTok{true}\NormalTok{)}
+\end{Highlighting}
+\end{Shaded}
+
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/final_box_plot.png}}
+
+And here is the final violin plot, with jitter and the same look and
+feel of the corporate boxplot.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\FunctionTok{puts}\NormalTok{ violin }\OperatorTok{+}\NormalTok{ decorations }\OperatorTok{+} \DataTypeTok{CorpTheme}\AttributeTok{.global\_theme}\NormalTok{(}\WarningTok{faceted:} \DecValTok{true}\NormalTok{)}
+\end{Highlighting}
+\end{Shaded}
+
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/final_violin_plot.png}}
+
+\subsection{Another View}\label{another-view}
+
+We now make another plot, with the same look and feel as before but
+facetted by dose and not by supplement. This shows how easy it is to
+create new plots by just changing small statement on the \emph{grammar
+of graphics}.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\NormalTok{caption }\OperatorTok{=} \OperatorTok{\textless{}\textless{}{-}}\ControlFlowTok{EOT}
+\DocumentationTok{Length of odontoblasts in 60 guinea pigs. }
+\DocumentationTok{Each animal received one of three dose levels of vitamin C.}
+\ControlFlowTok{EOT}
+
+\NormalTok{bp }\OperatorTok{=}\NormalTok{ tooth\_growth}\AttributeTok{.ggplot}\NormalTok{(}\ConstantTok{E}\AttributeTok{.aes}\NormalTok{(}\WarningTok{x:} \WarningTok{:supp}\NormalTok{, }\WarningTok{y:} \WarningTok{:len}\NormalTok{, }\WarningTok{group:} \WarningTok{:supp}\NormalTok{)) }\OperatorTok{+} 
+     \ConstantTok{R}\AttributeTok{.geom\_boxplot}\NormalTok{(}\ConstantTok{E}\AttributeTok{.aes}\NormalTok{(}\WarningTok{fill:} \WarningTok{:supp}\NormalTok{)) }\OperatorTok{+} \ConstantTok{R}\AttributeTok{.facet\_grid}\NormalTok{(}\WarningTok{:all}\AttributeTok{.til} \OperatorTok{:}\NormalTok{dose) }\OperatorTok{+}
+     \ConstantTok{R}\AttributeTok{.scale\_fill\_manual}\NormalTok{(}\WarningTok{values:} \ConstantTok{R}\AttributeTok{.c}\NormalTok{(}\StringTok{"cyan"}\NormalTok{, }\StringTok{"deepskyblue4"}\NormalTok{)) }\OperatorTok{+}
+     \ConstantTok{R}\AttributeTok{.labs}\NormalTok{(}\WarningTok{title:} \StringTok{"Tooth Growth:  Length by Dose"}\NormalTok{,}
+            \WarningTok{subtitle:} \StringTok{"Faceted by dose"}\NormalTok{,}
+            \WarningTok{x:} \StringTok{"Delivery method"}\NormalTok{, }\WarningTok{y:} \StringTok{"Teeth length"}\NormalTok{,}
+            \WarningTok{caption:}\NormalTok{ caption) }\OperatorTok{+}
+     \DataTypeTok{CorpTheme}\AttributeTok{.global\_theme}\NormalTok{(}\WarningTok{faceted:} \DecValTok{true}\NormalTok{)}
+
+\FunctionTok{puts}\NormalTok{ bp}
+\end{Highlighting}
+\end{Shaded}
+
+\pandocbounded{\includegraphics[keepaspectratio]{ruby_plot_files/figure-latex/facet_by_dose.png}}
+
+\section{Conclusion}\label{conclusion}
+
+In this article, we introduce Galaaz and show how to tightly couple Ruby
+and R in a way that Ruby developers do not need to be aware of the
+executing R engine. For the Ruby developer the existence of R is of no
+consequence, she is just coding in Ruby. On the other hand, for the R
+developer, migration to Ruby is a matter of small syntactic changes with
+a very gentle learning curve. As the R developer becomes more proficient
+in Ruby, he can start using `classes', `modules', `procs', `lambdas'.
+
+Trying to bring to Ruby the power of R starting from scratch is an
+enormous endeavour and would probably never be accomplished. Today's
+data scientists would certainly stick with either Python or R. Now, both
+the Ruby and R communities can benefit from this marriage:
+\textbf{Galaaz 2.0} uses \textbf{standard GNU R} for statistics and
+graphics and \textbf{JRuby} for application code, threading, and the JVM
+ecosystem. We presented the process to couple Ruby and R; the coupling
+is implemented by the Galaaz bridge and \textbf{gKnit} for literate
+documents, not by a single GraalVM polyglot runtime.
+
+For performance, expect \textbf{ordinary GNU R} behaviour for model
+fitting and plotting, while \textbf{JRuby} gives \textbf{real parallel
+threads} on the Ruby side and access to Java libraries when you need
+them.
+
+This article has shown how to improve a plot step-by-step. Starting from
+a very simple boxplot with all default configurations, we moved slowly
+to our final plot. The important point here is not if the final plot is
+actually beautiful (as beauty is in the eye of the beholder), but that
+there is a process of small steps improvements that can be followed to
+getting a final plot ready for presentation.
+
+Finally, this whole article was written in rmarkdown and compiled to
+HTML by \emph{gknit}, an application that wraps \emph{knitr} and allows
+documenting Ruby code. This application can be of great help for any
+Rubyist trying to write articles, blogs or documentation for Ruby.
+
+\section{Installing Galaaz}\label{installing-galaaz}
+
+\subsection{Prerequisites (Galaaz 2.0)}\label{prerequisites-galaaz-2.0}
+
+\begin{itemize}
+\tightlist
+\item
+  \textbf{JRuby} --- Ruby on the JVM
+  (\href{https://www.jruby.org/}{jruby.org})
+\item
+  A \textbf{JDK} compatible with your JRuby version
+\item
+  \textbf{GNU R} --- \texttt{R} on your \texttt{PATH}, with
+  compilers/tools available if packages must be built from source
+\end{itemize}
+
+The following R packages will be automatically installed when necessary,
+but could be installed prior to using gKnit if desired:
+
+\begin{itemize}
+\tightlist
+\item
+  ggplot2
+\item
+  gridExtra
+\item
+  knitr
+\end{itemize}
+
+Installation of R packages requires a development environment and can be
+time consuming. On Linux, the usual build tools (e.g.~a C/C++ compiler)
+are typically enough. On macOS, Xcode command-line tools are commonly
+required.
+
+\subsection{Preparation}\label{preparation}
+
+\begin{itemize}
+\tightlist
+\item
+  Install the \textbf{galaaz} gem (from RubyGems when published, or
+  \texttt{gem\ build} / \texttt{path:} from a checkout).
+\end{itemize}
+
+\subsection{Usage}\label{usage}
+
+\begin{itemize}
+\tightlist
+\item
+  From the Galaaz repository (or your installed layout), render
+  documents with \textbf{\texttt{bin/gknit}} (see the project manual for
+  flags such as \texttt{-\/-output\_format\ all}).
+\item
+  In Ruby code:
+  \texttt{require\ \textquotesingle{}galaaz\textquotesingle{}}
+\item
+  For running scripts with the correct JRuby and JVM options, use
+  \textbf{\texttt{bin/galaaz-jruby}} as described in the manual.
+\end{itemize}
+
+\end{document}