galaaz 0.4.2 → 0.4.5

data/blogs/ruby_plot/ruby_plot.tex

@@ -1,4 +1,4 @@
-\documentclass[]{article}
+\documentclass[11pt,]{article}
 \usepackage{lmodern}
 \usepackage{amssymb,amsmath}
 \usepackage{ifxetex,ifluatex}
@@ -24,8 +24,8 @@
 \usepackage[margin=1in]{geometry}
 \usepackage{hyperref}
 \hypersetup{unicode=true,
-            pdftitle={High Quality Scientific Plotting with Ruby in GraalVM},
-            pdfauthor={Rodrigo Botafogo},
+            pdftitle={How to make Beautiful Ruby Plots with Galaaz},
+            pdfauthor={Rodrigo Botafogo; Daniel Mossé; University of Pittsburgh},
             pdfborder={0 0 0},
             breaklinks=true}
 \urlstyle{same}  % don't use monospace font for urls
@@ -114,16 +114,15 @@
 
 \setlength{\droptitle}{-2em}
 
-  \title{High Quality Scientific Plotting with Ruby in GraalVM}
+  \title{How to make Beautiful Ruby Plots with Galaaz}
     \pretitle{\vspace{\droptitle}\centering\huge}
   \posttitle{\par}
-  \subtitle{Also: Allowing R to use classes, modules, blocks, etc.}
-  \author{Rodrigo Botafogo}
+    \author{Rodrigo Botafogo \\ Daniel Mossé \\ University of Pittsburgh}
     \preauthor{\centering\large\emph}
   \postauthor{\par}
       \predate{\centering\large\emph}
   \postdate{\par}
-    \date{19 October 2018}
+    \date{November 19th, 2018}
 
 % usar portugues do Brasil
 % \usepackage[brazilian]{babel}
@@ -132,7 +131,7 @@
 \usepackage{geometry}
 \geometry{a4paper, top=1in}
 
-% necessários para uso com kableExtra
+% needed for kableExtra
 \usepackage{longtable}
 \usepackage{multirow}
 \usepackage[table]{xcolor}
@@ -149,17 +148,38 @@
 \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}
-\fancyhf{}
 
-\usepackage{lipsum}
+% 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.
 
-% disponibilizar o comando lastpage
+% \usepackage{lipsum}
+
+% make available command lastpage
 \usepackage{lastpage}
 
-% tamanho do font padrão 11pt
-\usepackage[fontsize=10pt]{scrextend}
+% default fontsize 11pt better to add
+% fontsize on the yaml header
+% \usepackage[fontsize=11pt]{scrextend}
 
 % comandos para formatar uma tabela
 \usepackage{array}
@@ -167,147 +187,174 @@
 \newcolumntype{C}[1]{>{\centering\let\newline\\\arraybackslash\hspace{0pt}}m{#1}}
 \newcolumntype{R}[1]{>{\raggedleft\let\newline\\\arraybackslash\hspace{0pt}}m{#1}}
 
-% necessário para importar outros arquivos latex
+% 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}}
 
 \begin{document}
 \maketitle
 
+{
+\setcounter{tocdepth}{2}
+\tableofcontents
+}
 \section{Introduction}\label{introduction}
 
-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 which was first
-release circa 2005 and makes extensive use of Ruby's metaprogramming
-features. With the advend of RoR, Ruby became extremely popular and it
-peeked in popularity around 2008 according to the Tiobe index
-(\url{https://www.tiobe.com/tiobe-index/ruby/}). From 2008 to 2015, it's
-popularity declined consistently and then started picking up again
-during the next 3 years. At the time of this writing (November 2018),
-Ruby is ranked 16th in the Tiobe index.
-
-Python, considered a similar language to Ruby with similar features
-ranks 4th in the index. The first three positions are taken by Java, C
-and C++. One criticism often heard about Ruby, is that it is useful only
-for web applications while Python, with similar features has more
-diverse libraries, being useful for web applications with the Django
-framework, but also for scientific applications such as statistics, data
-analysis, big data, biology, etc. This criticism is by no way wrong.
-Although Ruby can do much more than just web applications:
-\url{https://github.com/markets/awesome-ruby}, for scientific computing,
-Ruby lags way behind Python and R, the two most prestigous languages in
-the field, with R being prefered by statisticians while Python is
-prefered by everyone else, because of it's gentle learning curve and
-more ``natural'' programming paradigm.
+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 it's popularity 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.
+
+Python, a similar language 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 and have even the most basic scientific computing infrastructure.
-Comes GraalVM into the picture:
+gap. Implementing a complete scientific computing infrastructure would
+take too long. Comes GraalVM into the picture:
 
-\begin{verbatim}
- GraalVM is a universal virtual machine for running applications written in JavaScript,
- Python 3, Ruby, R, JVM-based languages like Java, Scala, Kotlin, and LLVM-based languages
- such as C and C++.
+\begin{quote}
+GraalVM is a universal virtual machine for running applications written
+in JavaScript, Python 3, Ruby, R, JVM-based languages like Java, Scala,
+Kotlin, and LLVM-based languages such as C and C++.
 
- GraalVM removes the isolation between programming languages and enables interoperability in a
- shared runtime. It can run either standalone or in the context of OpenJDK, Node.js,
- Oracle Database, or MySQL.
+GraalVM removes the isolation between programming languages and enables
+interoperability in a shared runtime. It can run either standalone or in
+the context of OpenJDK, Node.js, Oracle Database, or MySQL.
 
- GraalVM allows you to write polyglot applications with a seamless way to pass values from one
- language to another. With GraalVM there is no copying or marshaling necessary as it is with
- other polyglot systems. This lets you achieve high performance when language boundaries are
- crossed. Most of the time there is no additional cost for crossing a language boundary at all.
+GraalVM allows you to write polyglot applications with a seamless way to
+pass values from one language to another. With GraalVM there is no
+copying or marshaling necessary as it is with other polyglot systems.
+This lets you achieve high performance when language boundaries are
+crossed. Most of the time there is no additional cost for crossing a
+language boundary at all.
 
- Often developers have to make uncomfortable compromises that require them to rewrite
- their software in other languages. For example:
+Often developers have to make uncomfortable compromises that require
+them to rewrite their software in other languages. For example:
 
-  * “That library is not available in my language. I need to rewrite it.” 
-  * “That language would be the perfect fit for my problem, but we cannot run it
-    in our environment.” 
-  * “That problem is already solved in my language, but the language is too slow.”
+\begin{itemize}
+\tightlist
+\item
+  That library is not available in my language. I need to rewrite it.
+\item
+  That language would be the perfect fit for my problem, but we cannot
+  run it in our environment.
+\item
+  That problem is already solved in my language, but the language is too
+  slow.
+\end{itemize}
 
-With GraalVM we aim to allow developers to freely choose the right language for the task at
-hand without making compromises.
-\end{verbatim}
+With GraalVM we aim to allow developers to freely choose the right
+language for the task at hand without making compromises.
+\end{quote}
 
 As stated above, GraalVM is a \emph{universal} virtual machine that
 allows Ruby and R (and other languages) to run on the same environment.
 GraalVM allows polyglot applications to \emph{seamlessly} interact with
-one another and pass values from one language to the other. Based on
-GraalVM, the Galaaz project was started. Galaaz indends to tightly
-couple Ruby and R and allow those languages to \emph{seamlessly}
-interact in a way that the user will be unaware of such interaction.
-
-Library wrapping is an usual way of bringing features from one library
-into another language. For instance, whenever Python needs to perform
-operations efficiently, C libraries are wrapped in Python. For the
-Python developer, the existence of such C library is of no concern. The
-problem with library wrapping is that for any new library of interest,
-there is the need to hand craft a new wrapper. With Galaaz, the same
-concept of wrapping was done, but instead of wrapping a single C or R
-library, Galaaz wraps the whole of the R language. Doing so, all
-thousands of R libraries are immediately available to Ruby developers
-and any new library developed in R will also become available without
-requiring a new wrapping effort.
-
-In this article, the graphing ggplot2 library from R will be accessed by
-Ruby transparently, bringing to Ruby the power of high quality
-scientific plotting. It might seem, from the exposed above, that Galaaz
-mainly benefits Ruby developers and might be of no consequence to the R
-developer. This article will however show that migrating from R to Ruby
-with Galaaz is a matter of small syntactic changes. Furthermore, R lacks
-some fundamental constructs for code reuse and large system
-construction. Using Galaaz, the R developer can easily migrate to a
-powerful OO language, at virtually no cost and then, as needs requires,
-she can add them to her toolbox.
+one another and pass values from one language to the other. Galaaz, a
+gem for Ruby, intends to tightly couple Ruby and R and allow those
+languages to interact in a way that the user will be unaware of such
+interaction.
+
+Library wrapping is an 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 of no concern. 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 of
+the R language in Ruby. Doing so, all thousands of R libraries are
+available to Ruby developers. Also any new library developed in R will
+be available without a new wrapping effort.
+
+This article shows how Ruby can use R's ggplot2 library tranparantly,
+and bring to Ruby the power of high quality scientific plotting. it also
+shows that migrating from R to Ruby with Galaaz is a matter of small
+syntactic changes. Using Ruby, the R developer can use all of Ruby's
+powerful OO features. It also becomes much easier to move code from the
+analysis phase to the production phase.
 
 In this article we will explore the R ToothGrowth dataset. In doing so,
-we will create some plots. Furthermore we will create a ``Corporate
-Template'' for our plots ensuring that any plot of the same type will
-have a consistent visualisation.
+we will create some boxplots. A primer on boxplot is available in
+\href{https://towardsdatascience.com/understanding-boxplots-5e2df7bcbd51}{this
+article}.
 
-\section{gKnit}\label{gknit}
+We will also create a Corporate Template ensuring that plots will have a
+consistent visualization. This template is build 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. Ruby
+modules are standard to the language and don't need special knowledge.
+
+In
+\href{https://towardsdatascience.com/ruby-plotting-with-galaaz-an-example-of-tightly-coupling-ruby-and-r-in-graalvm-520b69e21021}{this
+blog} we show a scatter plot in Ruby also with Galaaz.
 
-This document was written using rmarkdown and the corresponding HTML was
-generated by the gKnit application. gKnit is a wrapper around the
-powerful `knitr' application which converts rmarkdown text to many
-different output formats such as HTML, Latex, docx, etc. The gKnit tool
-is still under active development and will soon be released.
+\section{gKnit}\label{gknit}
 
-In rmarkdown, text and code can be part of the same document, and code
-blocks are marked with a special markup. Interested readers can easily
-google `knitr' and `rmarkdown'. in gKnit, each Ruby block is evaluated
-independently and `eval' in Ruby creates a new scope, so, in order for a
-variable defined in a block to be accessible in another block, it has to
-be a global variable, preceded by the `\$' sign.
+\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. In gKnit each Ruby
+chunk executes in its own scope and thus, local variable defined in a
+chunk are not accessible by other chunks. Yet, All chunks execute in the
+scope of a `chunk' class and instance variables (`@'), are available in
+all chunks.
 
 \section{Exploring the Dataset}\label{exploring-the-dataset}
 
-Let start by exploring our selected dataset. In this dataset the
-response is the length of odontoblasts (cells responsible for tooth
-growth) in 60 guinea pigs. 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 or ascorbic acid (a form of vitamin C and coded as VC).
-
-In Galaaz, in order to have access to an R variable pointed by an R
-symbol we use the corresponding Ruby symbol preceeded by the tilda
-(`\textasciitilde{}') function.
+Let's start by exploring our selected dataset. ToothGrowth is an R
+dataset. A dataset is like an excel spreadsheet, but 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 analyses 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, to
+have access to an R variable we use the corresponding Ruby symbol
+preceeded by the tilda (`\textasciitilde{}') function. Note in the
+following chunk that Ruby's `@tooth\_growth' is assigned the value of
+`\textasciitilde{}:ToothGrowth'. `ToothGrowth' is the R variable
+containing the dataset of interest.
 
 \begin{Shaded}
 \begin{Highlighting}[]
 \CommentTok{# Read the R ToothGrowth variable and assign it to the}
-\CommentTok{# Ruby tooth_growth variable}
-\DataTypeTok{$tooth_growth}\NormalTok{ = ~}\StringTok{:ToothGrowth}
-\CommentTok{# convert the dose to a factor}
-\DataTypeTok{$tooth_growth}\NormalTok{.dose = }\DataTypeTok{$tooth_growth}\NormalTok{.dose.as__factor}
-
+\CommentTok{# Ruby instance variable @tooth_growth that will be }
+\CommentTok{# available to all Ruby chunks in this document.}
+\OtherTok{@tooth_growth}\NormalTok{ = ~}\StringTok{:ToothGrowth}
 \CommentTok{# print the first few elements of the dataset}
-\NormalTok{puts }\DataTypeTok{$tooth_growth}\NormalTok{.head}
+\NormalTok{puts }\OtherTok{@tooth_growth}\NormalTok{.head}
 \end{Highlighting}
 \end{Shaded}
 
@@ -322,25 +369,86 @@ symbol we use the corresponding Ruby symbol preceeded by the tilda
 \end{verbatim}
 
 Great! We've managed to read the ToothGrowth dataset and take a look at
-its elements. Observe that we have three columns in this dataset: `len',
-`supp' and `dose'. Accessing a column, for example the `len' column, is
-done by doing `\$tooth\_growth.len'.
+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 'len' column and print the first few}
+\CommentTok{# elements of this column with the 'head' method.}
+\NormalTok{puts }\OtherTok{@tooth_growth}\NormalTok{.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 wiht either, 0.5, 1 or 2.
+Although 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}
+\OtherTok{@tooth_growth}\NormalTok{.dose = }\OtherTok{@tooth_growth}\NormalTok{.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}[]
-\NormalTok{puts }\DataTypeTok{$tooth_growth}\NormalTok{.dim}
-\CommentTok{# chdck why NULL}
-\NormalTok{puts R.str(}\StringTok{:ToothGrowth}\NormalTok{)}
-\NormalTok{puts }\DataTypeTok{$tooth_growth}\NormalTok{.summary}
+\NormalTok{puts }\OtherTok{@tooth_growth}\NormalTok{.dim}
 \end{Highlighting}
 \end{Shaded}
 
 \begin{verbatim}
 ## [1] 60  3
-## NULL
+\end{verbatim}
+
+This dataset has 60 rows, one for each subject and 3 columns, as we have
+already seen.
+
+Note that we do not 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}[]
+\OtherTok{@tooth_growth}\NormalTok{.str}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{verbatim}
+## 'data.frame':    60 obs. of  3 variables:
+##  $ len : num  4.2 11.5 7.3 5.8 6.4 10 11.2 11.2 5.2 7 ...
+##  $ supp: Factor w/ 2 levels "OJ","VC": 2 2 2 2 2 2 2 2 2 2 ...
+##  $ dose: Factor w/ 3 levels "0.5","1","2": 1 1 1 1 1 1 1 1 1 1 ...
+\end{verbatim}
+
+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}[]
+\NormalTok{puts }\OtherTok{@tooth_growth}\NormalTok{.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  
@@ -350,45 +458,55 @@ look at its dimensions, structure and summary statistics.
 ##  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 Rubyist that have never seen or used ggplot2, here is the
-description found on ggplot home page:
+description of ggplot found on its home page:
 
-\begin{verbatim}
-"ggplot2 is a system for declaratively creating graphics, based on _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{verbatim}
+\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} each
-component of the plot such as the grid, the axis, the data, title,
-subtitle, etc. is added to the plot in layers to form the final
-graphics.
-
-In this plot bellow, the `dose' is plotted on the `x' axis and the tooth
-length on the `y' axis. Note the specification in the the `aes' method:
-`E.aes(x: :dose, y: :len)', where `:dose' is the `dose' column of the
-dataset and `:len' the `len' column. The `aes' method is the
-\emph{aesthetics} for this plot. Then, to this layer, the
-`geom\_boxplot' is added and the whole plot is printed.
+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{},\ ...)}. In Galaaz, 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 Ruby
+like. The plot specifies the `dose' on the \(x\) axis and the `length'
+on the \(y\) axis with the `aes' method. `E.aes(x: :dose, y: :len)'. To
+specify the type of plot to create add a geom to the plot. For a
+boxplot, the geom is R.geom\_boxplot.
 
 Note also that we have a call to `R.png' before plotting and
 'R.dev\_\_off' after the print statement. `R.png' opens a `png' device
-for writing the plot. When 'R.dev\_\_off' is called, the device is
-closed and a `png' file is created. If no name is given to the `png'
-function, a file named `Rplot' is generated, where is the number of the
-plot. So, this first plot is called `Rplot001.png'. We can then include
-the generated `png' file in this document, by adding an rmarkdown
+for outputting the plot. 'R.dev\_\_off' closes the device and creates
+the `png' file. If we do no pass a name to the `png' function, the image
+gets a default name of `Rplot\textless{}nnn\textgreater{}' where
+\textless{}nnn\textgreater{} is the number of the plot. We can then
+include the generated `png' file in the document by adding an rmarkdown
 directive.
 
 \begin{Shaded}
 \begin{Highlighting}[]
 \NormalTok{require }\StringTok{'ggplot'}
 
-\NormalTok{R.png}
+\NormalTok{R.png(}\StringTok{"figures/dose_len.png"}\NormalTok{)}
 
-\NormalTok{e = }\DataTypeTok{$tooth_growth}\NormalTok{.ggplot(E.aes(}\StringTok{x: :dose}\NormalTok{, }\StringTok{y: :len}\NormalTok{))}
+\NormalTok{e = }\OtherTok{@tooth_growth}\NormalTok{.ggplot(E.aes(}\StringTok{x: :dose}\NormalTok{, }\StringTok{y: :len}\NormalTok{))}
 \NormalTok{print e + R.geom_boxplot}
 
 \NormalTok{R.dev__off}
@@ -397,16 +515,514 @@ directive.
 
 \begin{figure}
 \centering
-\includegraphics{Rplot001.png}
-\caption{ToothGrowth}
+\includegraphics[width=0.70000\textwidth]{figures/dose_len.png}
+\caption{}
+\end{figure}
+
+Great! We've just managed to create and save our first plot in Ruby with
+only four lines of code. We can 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 explicits 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, formulas are written a bit differently than in R. The
+following changes are necessary:
+
+\begin{itemize}
+\tightlist
+\item
+  R symbols are represented by the same Ruby symbol prefixed with the
+  `+' method. The symbol \texttt{x} in R becomes \texttt{+:x} in Ruby;
+\item
+  The `\textasciitilde{}' operator in R becomes `=\textasciitilde{}' in
+  Ruby. The formula \texttt{x\ \textasciitilde{}\ y} in R is written as
+  \texttt{+:x\ =\textasciitilde{}\ +:y} in Ruby;
+\item
+  The `.' symbol in R becomes `+:all'
+\end{itemize}
+
+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\ =\textasciitilde{}\ +: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\ =\textasciitilde{}\ +:all} would split the
+plot horizontally.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\NormalTok{R.png(}\StringTok{"figures/facet_by_delivery.png"}\NormalTok{)}
+
+\OtherTok{@base_tooth}\NormalTok{ = }\OtherTok{@tooth_growth}\NormalTok{.ggplot(E.aes(}\StringTok{x: :dose}\NormalTok{, }\StringTok{y: :len}\NormalTok{, }\StringTok{group: :dose}\NormalTok{))}
+
+\OtherTok{@bp}\NormalTok{ = }\OtherTok{@base_tooth}\NormalTok{ + R.geom_boxplot +}
+      \CommentTok{# Split in vertical direction}
+\NormalTok{      R.facet_grid(+}\StringTok{:all}\NormalTok{ =~ +}\StringTok{:supp}\NormalTok{)}
+      
+\NormalTok{puts }\OtherTok{@bp}
+
+\NormalTok{R.dev__off}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{figure}
+\centering
+\includegraphics[width=0.70000\textwidth]{figures/facet_by_delivery.png}
+\caption{}
 \end{figure}
 
-We've just managed to generate our first plot in Ruby with only two
-lines of code. This plot, however, if far from being pleasing to the
-eye.
+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 this paper was about data analysis, we should make a better analysis
+of the trends and should improve the statistical analysis. But 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{R.png(}\StringTok{"figures/facets_by_delivery_color.png"}\NormalTok{)}
+
+\OtherTok{@bp}\NormalTok{ = }\OtherTok{@bp}\NormalTok{ + R.geom_boxplot(E.aes(}\StringTok{fill: :dose}\NormalTok{))}
+\NormalTok{puts }\OtherTok{@bp}
+
+\NormalTok{R.dev__off}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{figure}
+\centering
+\includegraphics[width=0.70000\textwidth]{figures/facets_by_delivery_color.png}
+\caption{}
+\end{figure}
+
+Facetting helps us compare the general trends in the (OJ) and (VC)
+delivery methods. Adding color allow us to compare specifically how each
+dosage impacts the teeth 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 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 is going
+on on those boxes. 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 then 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}[]
+\NormalTok{R.png(}\StringTok{"figures/facets_with_points.png"}\NormalTok{)}
+
+\CommentTok{# Split in vertical direction}
+\OtherTok{@bp}\NormalTok{ = }\OtherTok{@bp}\NormalTok{ + R.geom_point}
+
+\NormalTok{puts }\OtherTok{@bp}
+
+\NormalTok{R.dev__off}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{figure}
+\centering
+\includegraphics[width=0.70000\textwidth]{figures/facets_with_points.png}
+\caption{}
+\end{figure}
+
+Now we can see the actual distribution of all the 60 subject. 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. This adds
+randomness to the position of the points, making it easier to see all of
+then and preventing data hiding. We also add color and change the shape
+of the points, making them even easier to see.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\NormalTok{R.png(}\StringTok{"figures/facets_with_jitter.png"}\NormalTok{)}
+
+\CommentTok{# Split in vertical direction}
+\NormalTok{puts }\OtherTok{@bp}\NormalTok{ + R.geom_jitter(}\StringTok{shape: }\DecValTok{23}\NormalTok{, }\StringTok{color: "cyan3"}\NormalTok{, }\StringTok{size: }\DecValTok{1}\NormalTok{)}
+
+\NormalTok{R.dev__off}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{figure}
+\centering
+\includegraphics[width=0.70000\textwidth]{figures/facets_with_jitter.png}
+\caption{}
+\end{figure}
+
+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 was 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
+smaller value (0.5) is on the botton of the labels and (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{R.png(}\StringTok{"figures/facets_by_delivery_color2.png"}\NormalTok{)}
+
+\OtherTok{@bp}\NormalTok{ = }\OtherTok{@bp}\NormalTok{ +}
+\NormalTok{      R.scale_fill_manual(}\StringTok{values: }\NormalTok{R.c(}\StringTok{"cyan"}\NormalTok{, }\StringTok{"deepskyblue"}\NormalTok{, }\StringTok{"deepskyblue4"}\NormalTok{),}
+                          \StringTok{breaks: }\NormalTok{R.c(}\StringTok{"2"}\NormalTok{,}\StringTok{"1"}\NormalTok{,}\StringTok{"0.5"}\NormalTok{))}
+
+\NormalTok{puts }\OtherTok{@bp}
+
+\NormalTok{R.dev__off}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{figure}
+\centering
+\includegraphics[width=0.70000\textwidth]{figures/facets_by_delivery_color2.png}
+\caption{}
+\end{figure}
+
+\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{R.png(}\StringTok{"figures/violin_with_jitter.png"}\NormalTok{)}
+
+\OtherTok{@violin}\NormalTok{ = }\OtherTok{@base_tooth}\NormalTok{ + R.geom_violin(E.aes(}\StringTok{fill: :dose}\NormalTok{)) + }
+\NormalTok{   R.facet_grid(+}\StringTok{:all}\NormalTok{ =~ +}\StringTok{:supp}\NormalTok{) +}
+\NormalTok{   R.geom_jitter(}\StringTok{shape: }\DecValTok{23}\NormalTok{, }\StringTok{color: "cyan3"}\NormalTok{, }\StringTok{size: }\DecValTok{1}\NormalTok{) +}
+\NormalTok{   R.scale_fill_manual(}\StringTok{values: }\NormalTok{R.c(}\StringTok{"cyan"}\NormalTok{, }\StringTok{"deepskyblue"}\NormalTok{, }\StringTok{"deepskyblue4"}\NormalTok{),}
+                       \StringTok{breaks: }\NormalTok{R.c(}\StringTok{"2"}\NormalTok{,}\StringTok{"1"}\NormalTok{,}\StringTok{"0.5"}\NormalTok{))}
+
+\NormalTok{puts }\OtherTok{@violin}
+
+\NormalTok{R.dev__off}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{figure}
+\centering
+\includegraphics[width=0.70000\textwidth]{figures/violin_with_jitter.png}
+\caption{}
+\end{figure}
+
+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 axis 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 for width and height are
+480.
+
+The `labs' function adds require 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.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\NormalTok{R.png(}\StringTok{"figures/facets_with_decorations.png"}\NormalTok{, }\StringTok{width: }\DecValTok{540}\NormalTok{, }\StringTok{height: }\DecValTok{560}\NormalTok{)}
+
+\NormalTok{caption = <<-}\KeywordTok{EOT}
+\OtherTok{Length of odontoblasts in 60 guinea pigs. }
+\OtherTok{Each animal received one of three dose levels of vitamin C.}
+\KeywordTok{EOT}
+
+\OtherTok{@decorations}\NormalTok{ =}
+\NormalTok{  R.labs(}\StringTok{title: "Tooth Growth:  Length by Dose"}\NormalTok{,}
+         \StringTok{subtitle: "Faceted by delivery method, (OJ) or (VC)"}\NormalTok{,}
+         \StringTok{x: "Dose (mg)"}\NormalTok{, }\StringTok{y: "Teeth length"}\NormalTok{,}
+         \StringTok{caption: }\NormalTok{caption)}
+
+\NormalTok{puts }\OtherTok{@bp}\NormalTok{ + }\OtherTok{@decorations}
+
+\NormalTok{R.dev__off}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{figure}
+\centering
+\includegraphics[width=0.70000\textwidth]{figures/facets_with_decorations.png}
+\caption{}
+\end{figure}
+
+\subsection{The Corp Theme}\label{the-corp-theme}
+
+We are almost done. But the plot 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 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}[]
+\KeywordTok{module} \DataTypeTok{CorpTheme}
+
+\NormalTok{  R.install_and_loads }\StringTok{'RColorBrewer'}
+  
+  \CommentTok{#---------------------------------------------------------------------------------}
+  \CommentTok{# face can be  (1=plain, 2=bold, 3=italic, 4=bold-italic)}
+  \CommentTok{#---------------------------------------------------------------------------------}
+  
+  \KeywordTok{def} \DecValTok{self}\NormalTok{.text_element(size, }\StringTok{face: "plain"}\NormalTok{, }\StringTok{hjust: }\DecValTok{nil}\NormalTok{)}
+\NormalTok{    E.element_text(}\StringTok{color: "#000080"}\NormalTok{, }
+                   \StringTok{face: }\NormalTok{face,}
+                   \StringTok{size: }\NormalTok{size,}
+           \StringTok{hjust: }\NormalTok{hjust)}
+  \KeywordTok{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{#---------------------------------------------------------------------------------}
+  
+  \KeywordTok{def} \DecValTok{self}\NormalTok{.global_theme(faceted = }\DecValTok{false}\NormalTok{)}
+    
+\NormalTok{    R.options(}\StringTok{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 = R.theme(}\StringTok{panel__grid__major: }\NormalTok{E.element_blank())}
+    \CommentTok{# remove minor grids}
+\NormalTok{    gb = gb + R.theme(}\StringTok{panel__grid__minor: }\NormalTok{E.element_blank)}
+    \CommentTok{# gb = R.theme(panel__grid__minor: E.element_blank)}
+    \CommentTok{# remove border}
+\NormalTok{    gb = gb + R.theme(}\StringTok{panel__border: }\NormalTok{E.element_blank)}
+    \CommentTok{# remove background. When working with faceted graphs, the background makes}
+    \CommentTok{# it easier to see each facet, so leave it}
+\NormalTok{    gb = gb + R.theme(}\StringTok{panel__background: }\NormalTok{E.element_blank) }\KeywordTok{if}\NormalTok{ !faceted}
+    \CommentTok{# Change axis font}
+\NormalTok{    gb = gb + R.theme(}\StringTok{axis__text: }\NormalTok{text_element(}\DecValTok{8}\NormalTok{))}
+    \CommentTok{# change axis title font}
+\NormalTok{    gb = gb + R.theme(}\StringTok{axis__title: }\NormalTok{text_element(}\DecValTok{10}\NormalTok{, }\StringTok{face: "bold"}\NormalTok{, }\StringTok{hjust: }\DecValTok{1}\NormalTok{))}
+    \CommentTok{# change font of title}
+\NormalTok{    gb = gb + R.theme(}\StringTok{title: }\NormalTok{text_element(}\DecValTok{12}\NormalTok{, }\StringTok{face: "bold"}\NormalTok{))}
+    \CommentTok{# change font of subtitle}
+\NormalTok{    gb = gb + R.theme(}\StringTok{plot__subtitle: }\NormalTok{text_element(}\DecValTok{9}\NormalTok{))}
+    \CommentTok{# change font of captions}
+\NormalTok{    gb = gb + R.theme(}\StringTok{plot__caption: }\NormalTok{text_element(}\DecValTok{8}\NormalTok{))}
+
+  \KeywordTok{end}
+   
+\KeywordTok{end}
+\end{Highlighting}
+\end{Shaded}
+
+\subsection{Final Box Plot}\label{final-box-plot}
+
+Here is our final boxplot, without jitter.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\NormalTok{R.png(}\StringTok{"figures/final_box_plot.png"}\NormalTok{, }\StringTok{width: }\DecValTok{540}\NormalTok{, }\StringTok{height: }\DecValTok{560}\NormalTok{)}
+
+\NormalTok{puts }\OtherTok{@bp}\NormalTok{ + }\OtherTok{@decorations}\NormalTok{ + }\DataTypeTok{CorpTheme}\NormalTok{.global_theme(}\StringTok{faceted: }\DecValTok{true}\NormalTok{)}
+
+\NormalTok{R.dev__off}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{figure}
+\centering
+\includegraphics[width=0.70000\textwidth]{figures/final_box_plot.png}
+\caption{}
+\end{figure}
+
+\subsection{Final Violin Plot}\label{final-violin-plot}
+
+Here is the final violin plot, with jitter and the same look and feel of
+the corporate boxplot.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\NormalTok{R.png(}\StringTok{"figures/final_violin_plot.png"}\NormalTok{, }\StringTok{width: }\DecValTok{540}\NormalTok{, }\StringTok{height: }\DecValTok{560}\NormalTok{)}
+
+\NormalTok{puts }\OtherTok{@violin}\NormalTok{ + }\OtherTok{@decorations}\NormalTok{ + }\DataTypeTok{CorpTheme}\NormalTok{.global_theme(}\StringTok{faceted: }\DecValTok{true}\NormalTok{)}
+
+\NormalTok{R.dev__off}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{figure}
+\centering
+\includegraphics[width=0.70000\textwidth]{figures/final_violin_plot.png}
+\caption{}
+\end{figure}
+
+\subsection{Another View}\label{another-view}
+
+Finally, here is a last plot, with the same look and feel as before but
+facetted by dose and not by supplement.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\NormalTok{R.png(}\StringTok{"figures/facet_by_dose.png"}\NormalTok{, }\StringTok{width: }\DecValTok{540}\NormalTok{, }\StringTok{height: }\DecValTok{560}\NormalTok{)}
+
+\NormalTok{caption = <<-}\KeywordTok{EOT}
+\OtherTok{Length of odontoblasts in 60 guinea pigs. }
+\OtherTok{Each animal received one of three dose levels of vitamin C.}
+\KeywordTok{EOT}
+
+\OtherTok{@bp}\NormalTok{ = }\OtherTok{@tooth_growth}\NormalTok{.ggplot(E.aes(}\StringTok{x: :supp}\NormalTok{, }\StringTok{y: :len}\NormalTok{, }\StringTok{group: :supp}\NormalTok{)) + }
+\NormalTok{      R.geom_boxplot(E.aes(}\StringTok{fill: :supp}\NormalTok{)) + R.facet_grid(+}\StringTok{:all}\NormalTok{ =~ +}\StringTok{:dose}\NormalTok{) +}
+\NormalTok{      R.scale_fill_manual(}\StringTok{values: }\NormalTok{R.c(}\StringTok{"cyan"}\NormalTok{, }\StringTok{"deepskyblue4"}\NormalTok{)) +}
+\NormalTok{      R.labs(}\StringTok{title: "Tooth Growth:  Length by Dose"}\NormalTok{,}
+             \StringTok{subtitle: "Faceted by dose"}\NormalTok{,}
+             \StringTok{x: "Delivery method"}\NormalTok{, }\StringTok{y: "Teeth length"}\NormalTok{,}
+             \StringTok{caption: }\NormalTok{caption) +}
+      \DataTypeTok{CorpTheme}\NormalTok{.global_theme(}\StringTok{faceted: }\DecValTok{true}\NormalTok{)}
+\NormalTok{puts }\OtherTok{@bp}
+
+\NormalTok{R.dev__off}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{figure}
+\centering
+\includegraphics[width=0.70000\textwidth]{figures/facet_by_dose.png}
+\caption{}
+\end{figure}
 
 \section{Conclusion}\label{conclusion}
 
+Galaaz tightly couples 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. For her, she is just coding in
+Ruby. On the other hand, for the R developer, migration to Ruby is a
+matter of small syntactic changes and very gentle learning curve. As the
+R developer becomes more proficient in Ruby, he can start using
+`classes', `modules', `procs', `lambdas'.
+
+This coupling shows the power of GraalVM and Truffle polyglot
+environment. Trying to bring to Ruby the power of R starting from
+scratch is an enourmous 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 might benefit from
+this marriage. Also, the process to couple Ruby and R can be also be
+done to couple Ruby and JavaScript and maybe also Ruby and Python. In a
+polyglot world a \emph{uniglot} language might be extremely relevant.
+
+From the perspective of performance, GraalVM and Truffle promises
+improvements that could reach over 10 times, both for
+\href{https://medium.com/graalvm/faster-r-with-fastr-4b8db0e0dceb}{FastR}
+and for
+\href{https://rubykaigi.org/2018/presentations/eregontp.html}{TruffleRuby}.
+
+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, but that there is a process of small steps
+improvements that can be followed until 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}\label{prerequisites}
@@ -414,7 +1030,8 @@ eye.
 \begin{itemize}
 \tightlist
 \item
-  GraalVM (\textgreater{}= rc8)
+  GraalVM (\textgreater{}= rc8):
+  \url{https://github.com/oracle/graal/releases}
 \item
   TruffleRuby
 \item
@@ -452,6 +1069,8 @@ am not sure what is needed on the Mac.
 \tightlist
 \item
   gknit 
+\item
+  In a scrip add: require `galaaz'
 \end{itemize}