galaaz 0.4.1 → 0.4.2

data/blogs/ruby_plot/ruby_plot.tex

@@ -0,0 +1,458 @@
+\documentclass[]{article}
+\usepackage{lmodern}
+\usepackage{amssymb,amsmath}
+\usepackage{ifxetex,ifluatex}
+\usepackage{fixltx2e} % provides \textsubscript
+\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
+  \usepackage[T1]{fontenc}
+  \usepackage[utf8]{inputenc}
+\else % if luatex or xelatex
+  \ifxetex
+    \usepackage{mathspec}
+  \else
+    \usepackage{fontspec}
+  \fi
+  \defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase}
+\fi
+% use upquote if available, for straight quotes in verbatim environments
+\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
+% use microtype if available
+\IfFileExists{microtype.sty}{%
+\usepackage{microtype}
+\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
+}{}
+\usepackage[margin=1in]{geometry}
+\usepackage{hyperref}
+\hypersetup{unicode=true,
+            pdftitle={High Quality Scientific Plotting with Ruby in GraalVM},
+            pdfauthor={Rodrigo Botafogo},
+            pdfborder={0 0 0},
+            breaklinks=true}
+\urlstyle{same}  % don't use monospace font for urls
+\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{\KeywordTok}[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{\BaseNTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
+\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
+\newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
+\newcommand{\CharTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\SpecialCharTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
+\newcommand{\StringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\VerbatimStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\SpecialStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\ImportTok}[1]{#1}
+\newcommand{\CommentTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}}
+\newcommand{\DocumentationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\AnnotationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\CommentVarTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{#1}}
+\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
+\newcommand{\VariableTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
+\newcommand{\ControlFlowTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
+\newcommand{\OperatorTok}[1]{\textcolor[rgb]{0.81,0.36,0.00}{\textbf{#1}}}
+\newcommand{\BuiltInTok}[1]{#1}
+\newcommand{\ExtensionTok}[1]{#1}
+\newcommand{\PreprocessorTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}}
+\newcommand{\AttributeTok}[1]{\textcolor[rgb]{0.77,0.63,0.00}{#1}}
+\newcommand{\RegionMarkerTok}[1]{#1}
+\newcommand{\InformationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\WarningTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\AlertTok}[1]{\textcolor[rgb]{0.94,0.16,0.16}{#1}}
+\newcommand{\ErrorTok}[1]{\textcolor[rgb]{0.64,0.00,0.00}{\textbf{#1}}}
+\newcommand{\NormalTok}[1]{#1}
+\usepackage{graphicx,grffile}
+\makeatletter
+\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
+\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
+\makeatother
+% Scale images if necessary, so that they will not overflow the page
+% margins by default, and it is still possible to overwrite the defaults
+% using explicit options in \includegraphics[width, height, ...]{}
+\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
+\IfFileExists{parskip.sty}{%
+\usepackage{parskip}
+}{% else
+\setlength{\parindent}{0pt}
+\setlength{\parskip}{6pt plus 2pt minus 1pt}
+}
+\setlength{\emergencystretch}{3em}  % prevent overfull lines
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+\setcounter{secnumdepth}{5}
+% Redefines (sub)paragraphs to behave more like sections
+\ifx\paragraph\undefined\else
+\let\oldparagraph\paragraph
+\renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
+\fi
+\ifx\subparagraph\undefined\else
+\let\oldsubparagraph\subparagraph
+\renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
+\fi
+
+%%% Use protect on footnotes to avoid problems with footnotes in titles
+\let\rmarkdownfootnote\footnote%
+\def\footnote{\protect\rmarkdownfootnote}
+
+%%% Change title format to be more compact
+\usepackage{titling}
+
+% Create subtitle command for use in maketitle
+\newcommand{\subtitle}[1]{
+  \posttitle{
+    \begin{center}\large#1\end{center}
+    }
+}
+
+\setlength{\droptitle}{-2em}
+
+  \title{High Quality Scientific Plotting with Ruby in GraalVM}
+    \pretitle{\vspace{\droptitle}\centering\huge}
+  \posttitle{\par}
+  \subtitle{Also: Allowing R to use classes, modules, blocks, etc.}
+  \author{Rodrigo Botafogo}
+    \preauthor{\centering\large\emph}
+  \postauthor{\par}
+      \predate{\centering\large\emph}
+  \postdate{\par}
+    \date{19 October 2018}
+
+% usar portugues do Brasil
+% \usepackage[brazilian]{babel}
+\usepackage[utf8]{inputenc}
+
+\usepackage{geometry}
+\geometry{a4paper, top=1in}
+
+% necessários para uso com 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}
+\pagestyle{fancy}
+\fancyhf{}
+
+\usepackage{lipsum}
+
+% disponibilizar o comando lastpage
+\usepackage{lastpage}
+
+% tamanho do font padrão 11pt
+\usepackage[fontsize=10pt]{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 para importar outros arquivos latex
+\usepackage{import}
+
+\newcommand{\RtoLatex}[2]{\newcommand{#1}{#2}}
+%\newcommand{\atraso}[1]{\color{red} \textbf {Tempo desde a Assinatura do Contrato: #1 dias}}
+
+\begin{document}
+\maketitle
+
+\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.
+
+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:
+
+\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++.
+
+ 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.
+
+ 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.”
+
+With GraalVM we aim to allow developers to freely choose the right language for the task at
+hand without making compromises.
+\end{verbatim}
+
+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.
+
+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.
+
+\section{gKnit}\label{gknit}
+
+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.
+
+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.
+
+\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.
+
+\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{$tooth_growth}\NormalTok{.dose.as__factor}
+
+\CommentTok{# print the first few elements of the dataset}
+\NormalTok{puts }\DataTypeTok{$tooth_growth}\NormalTok{.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. 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'.
+
+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}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{verbatim}
+## [1] 60  3
+## NULL
+##       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}
+
+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:
+
+\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}
+
+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.
+
+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
+directive.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\NormalTok{require }\StringTok{'ggplot'}
+
+\NormalTok{R.png}
+
+\NormalTok{e = }\DataTypeTok{$tooth_growth}\NormalTok{.ggplot(E.aes(}\StringTok{x: :dose}\NormalTok{, }\StringTok{y: :len}\NormalTok{))}
+\NormalTok{print e + R.geom_boxplot}
+
+\NormalTok{R.dev__off}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{figure}
+\centering
+\includegraphics{Rplot001.png}
+\caption{ToothGrowth}
+\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.
+
+\section{Conclusion}\label{conclusion}
+
+\section{Installing Galaaz}\label{installing-galaaz}
+
+\subsection{Prerequisites}\label{prerequisites}
+
+\begin{itemize}
+\tightlist
+\item
+  GraalVM (\textgreater{}= rc8)
+\item
+  TruffleRuby
+\item
+  FastR
+\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. In Linux, the gnu compiler and tools should be enough. I
+am not sure what is needed on the Mac.
+
+\subsection{Preparation}\label{preparation}
+
+\begin{itemize}
+\tightlist
+\item
+  gem install galaaz
+\end{itemize}
+
+\subsection{Usage}\label{usage}
+
+\begin{itemize}
+\tightlist
+\item
+  gknit 
+\end{itemize}
+
+
+\end{document}