galaaz 0.4.9 → 0.4.10

data/blogs/ruby_plot/ruby_plot.tex

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-  \title{How to make Beautiful Ruby Plots with Galaaz}
-    \pretitle{\vspace{\droptitle}\centering\huge}
-  \posttitle{\par}
-    \author{Rodrigo Botafogo \\ Daniel Mossé \\ University of Pittsburgh}
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-    \date{November 19th, 2018}
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-\begin{document}
-\maketitle
-
-{
-\setcounter{tocdepth}{2}
-\tableofcontents
-}
-\section{Introduction}\label{introduction}
-
-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. Implementing a complete scientific computing infrastructure would
-take too long. Comes GraalVM into the picture:
-
-\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 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:
-
-\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{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. 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 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 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.
-
-\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. 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'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 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 }\OtherTok{@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. 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 }\OtherTok{@tooth_growth}\NormalTok{.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 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  
-##  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 Rubyist that have never seen or used ggplot2, here is the
-description of ggplot found on 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{},\ ...)}. 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 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(}\StringTok{"figures/dose_len.png"}\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}
-\end{Highlighting}
-\end{Shaded}
-
-\begin{figure}
-\centering
-\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}
-
-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}
-
-\begin{itemize}
-\tightlist
-\item
-  GraalVM (\textgreater{}= rc8):
-  \url{https://github.com/oracle/graal/releases}
-\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 
-\item
-  In a scrip add: require `galaaz'
-\end{itemize}
-
-
-\end{document}