Make exercise 3

module2/exo3/exercice_R_en.org

-#+TITLE:  Your title
-#+AUTHOR: Your name
-#+DATE:   Today's date
+#+TITLE: Plots in org mode
 #+LANGUAGE: en
-# #+PROPERTY: header-args :eval never-export
 
-#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/htmlize.css"/>
-#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/readtheorg.css"/>
-#+HTML_HEAD: <script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
-#+HTML_HEAD: <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
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-#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/readtheorg/js/readtheorg.js"></script>
-
-* Some explanations
-
-This is an org-mode document with code examples in R.  Once opened in
-Emacs, this document can easily be exported to HTML, PDF, and Office
-formats. For more information on org-mode, see
-https://orgmode.org/guide/.
-
-When you type the shortcut =C-c C-e h o=, this document will be
-exported as HTML. All the code in it will be re-executed, and the
-results will be retrieved and included into the exported document. If
-you do not want to re-execute all code each time, you can delete the #
-and the space before ~#+PROPERTY:~ in the header of this document.
-
-Like we showed in the video, R code is included as follows (and is
-exxecuted by typing ~C-c C-c~):
-
-#+begin_src R :results output :exports both
-print("Hello world!")
-#+end_src
+* Plotting
+
+First we put the dataset in a variable
+
+#+BEGIN_SRC R :results output :exports src :session *R* 
+y <- c(14.0, 7.6, 11.2, 12.8, 12.5, 9.9, 14.9, 9.4, 16.9,
+       10.2, 14.9, 18.1, 7.3, 9.8, 10.9,12.2, 9.9, 2.9, 2.8,
+       15.4, 15.7, 9.7, 13.1, 13.2, 12.3, 11.7, 16.0, 12.4,
+       17.9, 12.2, 16.2, 18.7, 8.9, 11.9, 12.1, 14.6, 12.1,
+       4.7, 3.9, 16.9, 16.8, 11.3, 14.4, 15.7, 14.0, 13.6,
+       18.0, 13.6, 19.9, 13.7, 17.0, 20.5, 9.9, 12.5, 13.2,
+       16.1, 13.5, 6.3, 6.4, 17.6, 19.1, 12.8, 15.5, 16.3,
+       15.2, 14.6, 19.1, 14.4, 21.4, 15.1, 19.6, 21.7, 11.3,
+       15.0, 14.3, 16.8, 14.0, 6.8, 8.2, 19.9, 20.4, 14.6,
+       16.4, 18.7, 16.8, 15.8, 20.4, 15.8, 22.4, 16.2, 20.3,
+       23.4, 12.1, 15.5, 15.4, 18.4, 15.7, 10.2, 8.9, 21.0)
+df <- data.frame(x = seq(0, length(y)-1), y = y)
+#+END_SRC
 
 #+RESULTS:
-: [1] "Hello world!"
 
-And now the same but in an R session. This is the most frequent
-situation, because R is really an interactive language. With a
-session, R's state, i.e. the values of all the variables, remains
-persistent from one code block to the next. The code is still executed
-using ~C-c C-c~.
+** Sequence plot
 
-#+begin_src R :results output :session *R* :exports both
-summary(cars)
-#+end_src
+#+BEGIN_SRC R :results output graphics :exports both :file ./sequence_plot.png :width 600 :height 400 :session *R* 
+library(ggplot2)
+ggplot(df, aes(x = x, y = y)) + 
+  geom_line() +
+  theme_bw()
+#+END_SRC
 
 #+RESULTS:
-:      speed           dist       
-:  Min.   : 4.0   Min.   :  2.00  
-:  1st Qu.:12.0   1st Qu.: 26.00  
-:  Median :15.0   Median : 36.00  
-:  Mean   :15.4   Mean   : 42.98  
-:  3rd Qu.:19.0   3rd Qu.: 56.00  
-:  Max.   :25.0   Max.   :120.00
-
-Finally, an example for graphical output:
-#+begin_src R :results output graphics :file "./cars.png" :exports results :width 600 :height 400 :session *R* 
-plot(cars)
-#+end_src
+[[file:./sequence_plot.png]]
 
-#+RESULTS:
-[[file:./cars.png]]
+** Histogram plot
 
-Note the parameter ~:exports results~, which indicates that the code
-will not appear in the exported document. We recommend that in the
-context of this MOOC, you always leave this parameter setting as
-~:exports both~, because we want your analyses to be perfectly
-transparent and reproducible.
+#+BEGIN_SRC R :results output graphics :exports both :file ./histogram_plot.png :width 600 :height 400 :session *R* 
+library(ggplot2)
+ggplot(df, aes(x = y)) + 
+  geom_histogram(bins=10) +
+  theme_bw()
+#+END_SRC
 
-Watch out: the figure generated by the code block is /not/ stored in
-the org document. It's a plain file, here named ~cars.png~. You have
-to commit it explicitly if you want your analysis to be legible and
-understandable on GitLab.
+#+RESULTS:
+[[file:./histogram_plot.png]]
 
-Finally, don't forget that we provide in the resource section of this
-MOOC a configuration with a few keyboard shortcuts that allow you to
-quickly create code blocks in R by typing ~<r~ or ~<R~ followed by
-~Tab~.
 
-Now it's your turn! You can delete all this information and replace it
-by your computational document.