Difference between revisions of "RPR-Shiny"

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R Shiny
 
R Shiny
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<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#f2fafa; font-size:30%; font-weight:200; color: #000000; ">
 
(Shiny; R Web Applications)
 
(Shiny; R Web Applications)
 
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<b>Abstract:</b><br />
 
<b>Abstract:</b><br />
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<b>Deliverables:</b><br />
 
<b>Deliverables:</b><br />
 
<section begin=deliverables />
 
<section begin=deliverables />
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<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-time_management" -->
+
<li><b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.</li>
−
*<b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
+
<li><b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.</li>
−
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-journal" -->
+
<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
−
*<b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.
 
−
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-insights" -->
 
−
*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
 
 
<section end=deliverables />
 
<section end=deliverables />
 
<!-- ============================  -->
 
<!-- ============================  -->
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{{STUB}}
  
 
{{Smallvspace}}
 
{{Smallvspace}}
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 +
=== Evaluation ===
 +
<b>Evaluation: NA</b><br />
 +
<div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div>
 
== Contents ==
 
== Contents ==
−
<!-- included from "./components/RPR-Shiny.components.txt", section: "contents" -->
 
 
[https://shiny.rstudio.com/ '''Shiny'''] is an R package that supports running R code as an interactive Web-page. It is a great asset in an environment where you need to support non-programming users to give them a flexible way to interact with data and explore it.
 
[https://shiny.rstudio.com/ '''Shiny'''] is an R package that supports running R code as an interactive Web-page. It is a great asset in an environment where you need to support non-programming users to give them a flexible way to interact with data and explore it.
  
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+
...
−
is an idea that software is best described in a natural language, focussing on the logic of the program, i.e. the '''why''' of code, not the '''what'''. The goal is to ensure that model, code, and documentation become a single unit, and that all this information is stored in one and only one location. The product should be ''consistent'' between its described goals and its implementation, ''seamless'' in capturing the process from start (data input) to end (visualization, interpretation), and ''reversible'' (between analysis, design and implementation).
 
−
 
 
−
In literate programming, narrative and computer code are kept in the same file. This source document is typically written in ''Markdown'' or ''LaTeX'' syntax and includes the programming code as well as text annotations, tables, formulas etc. The supporting software can '''weave''' human-readable documentation from this, or '''tangle''' executable code. Literate programming with both Markdown and LaTex is supported by '''R Studio''' and this makes the '''R Studio''' interface a useful development environment for this paradigm. While it is easy to edit source files with a different editor and process files in base '''R''' after loading the {{R|utils|Sweave()|Sweave()</code> and <code>Stangle()}} functions or the {{R|knitr}} package. In our context here we will use '''R Studio''' because it conveniently integrates the functionality we need.
 
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{{R|knitr}} is an '''R''' package for {{WP|literate programming}}. It is integrated with [http://www.rstudio.com '''R Studio'''].
 
  
 
{{Vspace}}
 
{{Vspace}}
  
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==RMarkdown==
 
−
 
−
Markdown is an extremely simple and informal way of structuring documents that is useful if for some reason you feel html is too complicated. That's really all it does: format documents in a simple way so they can be displayed as Web pages. For Markdown documentation, [http://daringfireball.net/projects/markdown/basics '''see here.''']. The concept is quite similar to Wiki markup syntax, the syntax is (regrettably) different, and for a number of features there there are (regrettably) several different ways to achieve the same results.
 
−
 
−
[http://rmarkdown.rstudio.com '''RMarkdown'''] is an '''R''' package that is integrated with '''R Studio''' and allows integrating '''R''' code with Markdown documents. knitr can work with Markdown files, and this gives additional output options, such as PDF and MSWord documents.
 
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−
 
−
Let's give it a try: we'll write and document an '''R''' function that will find us a random phobia to ponder on.
 
−
 
−
{{task|1=
 
−
* Open an '''R Studio''' session.
 
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* Select '''Session &rarr; Set Working Directory &rarr; Choose Directory...''' and choose some project directory.
 
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** <small>Note that there is a bug in '''R Studio''' that will prevent the knitr interface from working correctly '''if''' your home directory contains an <code>.Rprofile</code> file that issues a <code>setwd()</code> command to a directory other than your project directory. If you run into an error when ''weaving'' your file, remove any  <code>setwd()</code> command you might find in such a profile.</small>
 
−
* Select '''File &rarr; New File &rarr; RMarkdown...'''. When you do this the first time, '''R Studio''' will ask you whether you want to install/update a number of required packages. Click '''Yes'''.
 
−
* Enter "Random Phobia" as the '''Title''' and your name as the '''Author''', select to create a '''Document''', and check '''HTML''' as the default output option.
 
−
'''R Studio''' will load some default text and markup into the script pane which we can edit.
 
−
 
−
* Choose '''Help &rarr; Cheatssheets &rarr; R Markdown Cheat Sheet''' and '''R Markdown Reference Guide''' to download two PDFs via your browser. Browse the contents to get an idea where you can clarify concepts as you go through this example.
 
−
 
−
Let's introduce our plan: copy/paste the following text into the document to replace the two sections with the headers <code>## R Markdown</code> and <code>## Including Plots</code>.
 
−
 
−
<div class{{=}}"text-box">
 
−
<nowiki>##Phobias!</nowiki><br />
 
−
We all have some, but we could always use more. How to know them all? With this code we access the Oxford English Dictionary's Website - the most authoritative source on the English language, and scrape a list of phobias. A function is supplied to retrieve a random phobia, which we can subsequently ponder on - either to delight in the fact that we don't have that fear, or to add to our daily quota of anxieties &lt;small>(like our well-founded [fear of bad programming practice](<nowiki>http://xkcd.com/292/</nowiki>))&lt;/small>.
 
−
 
−
To load the list, we will "screenscrape" a list of Phobias from the [OED Phobia list](<nowiki>https://en.oxforddictionaries.com/explore/phobias-list</nowiki>). First, we load the `rvest` library (or install it from CRAN, if we don't have it).
 
−
 
−
</div>
 
−
 
−
Note the following Markdown elements in the code:
 
−
 
−
 
−
::- a tag <code>&lt;small>Text...&lt;/small></code> to set text to a smaller font size <small>(we could have used <code>&lt;span style&#61;"font-size:85%;">Text...&lt;/span></code> instead because Markdown respects HTML elelements)</small>;
 
−
 
−
::- a Web link <code>[Text...](URL)</code>added to text;
 
−
 
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::- backticks that cause text to be rendered as "code".
 
−
 
−
* The filename in the script pane tab (<span style="colour:#AA0000;">Untitled1</span>) is red, because the file contains unsaved changes. Save the file in your project directory under the name<code>RandomPhobia</code>, note that the extension <code>.Rmd</code> is automatically added.
 
−
 
−
Now click on the ''wool and knitting needle'' icon in the menu bar to compile this code to HTML and view the current state in the viewer pane. See how the elements are rendered.
 
−
 
−
Then it's time to add our first bit of '''R code'''
 
−
 
−
*Copy and paste the following:
 
−
 
−
<source lang="R">
 
−
```{r loadLibrary}
 
−
if (! require(rvest, quietly=TRUE)) {
 
−
  install.packages("rvest")
 
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  library(rvest)
 
−
}
 
−
```
 
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</source>
 
−
 
−
 
−
This is what is know as a "code chunk". It is delimited by three backticks <code>```</code> and has directives and options for the chunk in the first line. It is labelled as '''R''' code, and note that after the <code>{r </code> we have added an (optional) label for the chunk. That is useful, because we can rapidly navigate between chunks (click on the navigation menu at the ''bottom'' of the script pane), and we can refer to the labels to execute chunks that are coded later in the document at an earlier stage. This is an important idea of literate programming: the flow of the document should not be determined by the requirements of the code, but by the logic of the narrative.  '''TLDR;''' label your chunks. It's useful.
 
−
 
−
Other options can be added after a comma, for example we can suppress printing of a chunk into the document altogether, if we think it is not relevant for the document, by adding the option <code>echo{{=}}FALSE</code><ref>For a complete list of chunk options, see [http://yihui.name/knitr/options/ the documentation by knitr's author, Xie Yihui].</ref>.
 
−
 
−
* To execute a particular chunk, simply place the cursor into the chunk and select '''Chunks &rarr; Run Current Chunk''' from the menu at the top of the script pane. Try this and check the console pane, the library should load without error.
 
−
 
−
* Let's add more text and code: copy and paste this into the document to add more comment and a second chunk.
 
−
 
−
<div class{{=}}"text-box">
 
−
The `rvest` package was designed for screenscraping and has functions to make our life very easy: it accesses an URL, looks for all HTML formatted tables, parses them with an XPATH expression and returns them as lists from which we can get data frames. There may be several tables in the source page, each one is returned as a list element. Since we know (hope?) the OED page contains only one table, we use only the first list element.<br />
 
−
<source lang="R">
 
−
```{r getPageData, cache=TRUE}
 
−
phobias <- read_html("https://en.oxforddictionaries.com/explore/phobias-list")
 
−
phobias <- html_nodes(phobias, xpath = '//*[@id="content"]/div[1]/div[2]/div/div/div/div/div[4]/table')
 
−
phobias <- html_table(phobias)[[1]]
 
−
```
 
−
</source>
 
−
 
−
</div>
 
−
 
−
Some things to note here:
 
−
 
−
* Enclosing a piece of text in "backticks" <code>`Text...`</code> formats that text as "code" - typically in a fixed-width font.
 
−
* For this chunk we have set the option <code>cache</code> as <code>TRUE</code>. This is a very useful and well thought out mechanism that avoids recomputing code that takes a long time or should otherwise be limited. The results of a cached chunk of code are stored locally and retrieved when the file is ''weaved''. Only if anything within the chunk is changed (or <code>cache</code> is set to <code>FALSE</code>), is the chunk evaluated again. This prevents us from excessively pounding on the OED as we develop our script, which is a question of good manners in the context of this example, but can save a lot of time as our projects become large and the calculations become complex.
 
−
* <code>rvest</code> needs an XPATH expression to parse the document. Writing XPATH expressions can be a bit gnarly - the RBloggers article linked from the Further Reading section demonstrates a nifty way to get the expression from within a Chrome browser window. The interface has slightly changed since the article was written, but it's easy enough to figure out.
 
−
* If you examine the <code>phobias</code> dataframe, you may note that the columns are named x1 and x2, and that the column headers are in the first row of the dataframe. This is because the OED authors did not put their column headers in <code>&lt;th&gt;</code> tags, so  <code>html_table()</code> assumed they are part of the contents. You should fix this, use the first row as columnames and remove the first row. If you don't know how, you can peek below<ref>Add the follwing bit into the <code>getPageData</code> chunk:
 
−
<source lang="R">
 
−
colnames(phobias) <- phobias[1, ]
 
−
phobias <- phobias[-1, ]
 
−
</source></ref>.
 
−
 
−
In order to make sure everything has worked, we'll print a sample from the table to our documentation file. RMarkdown provides a shorthand notation for tables - just like Wiki markup. I never use these. HTML tables are easy enough to format and remember and they provide '''many''' more options. In the example below, we customize the row background-color for alternating rows. That is something we could not do with simple markdown.
 
−
 
−
*Paste the following:
 
−
 
−
<source lang="rsplus">
 
−
**Table**: seven random phobias
 
−
```{r renderPhobiaTable, echo=FALSE, results='asis'}
 
−
cat("<table border=\"1\", width=\"50%\">\n")
 
−
cat("<tr style=\"background-color:#CCFFF0;\"><th>Phobia</th><th>Fear of...</th></tr>\n")
 
−
for (i in 1:7) {
 
−
  r <- randRow(phobias)
 
−
  if (i %% 2) {
 
−
    cat("<tr style=\"background-color:#F9F9F9;\">")
 
−
  }
 
−
  else {
 
−
    cat("<tr style=\"background-color:#EEFFF9;\">")
 
−
  }
 
−
  cat(paste("<td>", r[2], "</td><td>", r[1], "</td></tr>\n", sep=""))
 
−
}
 
−
cat("</table>\n")
 
−
```
 
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</source>
 
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−
This is now a mix of markup code and '''R''' code. Two important options in the chunk header:
 
−
* <code>echo{{=}}FALSE</code> prevents the contents of the chunk to be printed. We don't want this code in our output, we only want the result.
 
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* <code>results{{=}}'asis'</code> prevents the results from being marked up. The raw HTML is sent to the output document.
 
−
 
−
But note the following: this piece of code calls a function <code>randRow(phobiaFrame)</code> that we have not defined yet. In an '''R''' script this would not work. But in a knitr document we can '''reference''' a chunk of code anywhere in (and outside) of the document and thus define our function before the <code>renderPhobiaTable</code> chunk is executed. This is important for literate programming, where we don't want to be constrained by the requirements of the code.
 
−
 
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Therefore, paste the following '''before''' the previous chunk:
 
−
 
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<source lang="rsplus">
 
−
 
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```{r , ref.label="randRow", echo=FALSE}
 
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```
 
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</source>
 
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This executes the code chunk with the label <code>randRow</code> (and - you guessed it - the function will be defined in that chunk) without giving any output.
 
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To finish off, paste the following:
 
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<div class{{=}}"text-box">
 
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&lt;p>&amp;nbsp;<br />
 
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&lt;p><br />
 
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To pick a single random phobia from the list, we take a (pseudo) random sample of size 1 from the number of rows in the `phobiaFrame` object. Our function thus returns a random row from a matrix or dataframe, and it uses an optional argument: `seed`. This can either be Boolean `FALSE` (the default), or an integer that is used in R's `set.seed()` function.
 
−
 
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<source lang="rsplus">
 
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```{r randRow}
 
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randRow <- function(M, seed = FALSE) {
 
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  # Return a random row from a dataframe M.
 
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  if (seed) {
 
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    set.seed(as.integer(seed))
 
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  }
 
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  return(M[sample(1:nrow(M), 1), ])
 
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}
 
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```
 
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</source>
 
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With this useful tool we can ponder on our favourite phobia of the day. For today, let it be **`r randRow(phobias, seed{{=}}1123581321)[2]`**, the fear of `r randRow(phobias, seed{{=}}1123581321)[1]`.
 
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Reptiles! Awful.
 
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</div>
 
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This piece now contains the function definition for <code>randRow</code>, which it prints to the document after our comments. It also contains '''inline''' '''R''' code that is executed as the document is built.
 
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* That should be all. You should be able to save the document and select (from the menu bar of the script pane) '''Knit &rarr; Knit to HTML''' to execute the code, build, and load a Webpage with the document we just wrote. If your code has errors in the chunks, they will be reported in the console.
 
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<small>If all the pasting of bits and chunks was confusing, the final <code>.Rmd</code> file is [http://steipe.biochemistry.utoronto.ca/abc/assets/RandomPhobia.Rmd here]. But it does not contain the fix for the first row.</small>
 
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}}
 
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{{Vspace}}
 
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==R Notebooks==
 
−
 
−
R Notebooks take the concpet into the RStudio editor itself, rather than constructing a Webpage. On one hand, you become dependent on the RStudio editor, on the other hand, you directly edit and comment as you are developing. This is '''true''' "Literate Programming".
 
−
 
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{{task|1=
 
−
Read about the concept [http://rmarkdown.rstudio.com/r_notebooks.html '''here'''] and follow along with the exercise.
 
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}}
 
−
 
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{{Vspace}}
 
  
 
== Self-evaluation ==
 
== Self-evaluation ==
  
 +
<!--
 
=== Question 1===
 
=== Question 1===
  
−
Add a histogram to the code that prints the length distribution of the phobia names. <small>(Hint: use the <code>nchar()</code> function.)</small>
+
Do this ... <small>(Hint: use the <code>nchar()</code> function.)</small>
  
 
<div class="toccolours mw-collapsible mw-collapsed" style="width:800px">
 
<div class="toccolours mw-collapsible mw-collapsed" style="width:800px">
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<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
  
−
<source lang="rsplus">
+
...
−
```{r showHist}
 
−
 
 
−
hist(nchar(phobias[ , 1]),
 
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    main = "Length of phobia-names",
 
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    xlab = "number of letters",
 
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    ylab = "counts",
 
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    col="paleturquoise")
 
−
 
 
−
```
 
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Done.
 
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</source>
 
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</div>
 
</div>
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== Notes ==
 
−
<!-- included from "./components/RPR-Shiny.components.txt", section: "notes" -->
 
−
<!-- included from "./data/ABC-unit_components.txt", section: "notes" -->
 
−
<references />
 
 
== Further reading, links and resources ==
 
== Further reading, links and resources ==
−
<div class="reference-box">[https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf R Markdown Reference Guide] (PDF @ RStudio)</div>
+
...
−
<div class="reference-box">[https://www.r-bloggers.com/using-rvest-to-scrape-an-html-table/ Using rvest to Scrape an HTML Table] (R Bloggers)</div>
 
−
{{Smallvspace}}
 
−
<div class="reference-box">[https://blog.ouseful.info/2017/11/15/programming-meh-lets-teach-how-to-write-computational-essays-instead/ Thoughts on notebooks and literate programming] (Tony Hirst, via R Bloggers)</div>
 
−
 
 
  
  
 
{{Vspace}}
 
{{Vspace}}
  
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−
<!-- included from "./data/ABC-unit_components.txt", section: "ABC-unit_ask" -->
 
−
 
−
----
 
−
 
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{{Vspace}}
 
−
 
−
<b>If in doubt, ask!</b> If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.
 
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----
 
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{{Vspace}}
 
  
 
<div class="about">
 
<div class="about">
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:2018-11-13
 
:2018-11-13
 
<b>Version:</b><br />
 
<b>Version:</b><br />
−
:1.0
+
:0.1
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
−
*1.0 First live version
+
*0.1 Stub only
 
</div>
 
</div>
−
[[Category:ABC-units]]
 
 
<!-- included from "./data/ABC-unit_components.txt", section: "ABC-unit_footer" -->
 
<!-- included from "./data/ABC-unit_components.txt", section: "ABC-unit_footer" -->
  
 
{{CC-BY}}
 
{{CC-BY}}
  
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[[Category:ABC-units]]
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{{UNIT}}
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{{STUB}}
 
</div>
 
</div>
 
<!-- [END] -->
 
<!-- [END] -->

Latest revision as of 09:29, 25 September 2020

R Shiny

(Shiny; R Web Applications)


 


Abstract:

Introduction to R Shiny apps

Objectives:
This unit will ...

  • ... introduce the principles of R Shiny apps;
  • ... teach the practice with an example app;
  • ... point you to additional information resources;

Outcomes:
After working through this unit you ...

  • ... can write a Shiny app and include it with your R package.

Deliverables:

  • Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
  • Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.
  • Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.

    • Prerequisites:


     


    Sorry!

    This page is only a stub; it is here as a placeholder to establish the logical framework of the site but there is no significant content as yet. Do not work with this material until it is updated to "live" status.


     



     


    Evaluation

    Evaluation: NA

    This unit is not evaluated for course marks.

    Contents

    Shiny is an R package that supports running R code as an interactive Web-page. It is a great asset in an environment where you need to support non-programming users to give them a flexible way to interact with data and explore it.

    ...


     


    Self-evaluation

    CreativeCommonsBy.png This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.

    Sorry!

    This page is only a stub; it is here as a placeholder to establish the logical framework of the site but there is no significant content as yet. Do not work with this material until it is updated to "live" status.

    Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=RPR-Shiny&oldid=11749"