Cheat Sheet R Markdown

Posted : admin On 12/8/2021
  • See the PDF chapter of the R Markdown book for some guidance with these. ^ I’m sure I could create a perfectly fine cheat sheet using just these options, or, even re-create the output that I have achieved with my template. ^ You can specify other options as well, such.
  • R Markdown:: CHEAT SHEET Open a new.Rmd file at File New File R Markdown. Use the wizard that opens to pre-populate the file with a template Write document by editing template Knit document to create report; use knit button or render to knit Preview Output in.
  • Since I’m using knitr and R markdown to create this webpage, in the code that follows I will include the stargazer option type = 'html'. Stargazer is set to produce LaTeX output by default. If you desire LaTeX output, just remove the type option from the code below. Also, while I have added an example for many of the available stargazer options, I have not included all of them.

Since I’m using knitr and R markdown to create this webpage, in the code that follows I will include the stargazer option type = 'html'. Stargazer is set to produce LaTeX output by default. If you desire LaTeX output, just remove the type option from the code below.

9 minute read

R Markdown Overview

R Markdown combines markdown (an easy to write plain text format) with embeddedR code chunks. When compiling R Markdown documents, the code components can beevaluated so that both the code and its output can be included in the finaldocument. This makes analysis reports highly reproducible by allowing to automaticallyregenerate them when the underlying R code or data changes. R Markdowndocuments (.Rmd files) can be rendered to various formats including HTML andPDF. The R code in an .Rmd document is processed by knitr, while theresulting .md file is rendered by pandoc to the final output formats(e.g. HTML or PDF). Historically, R Markdown is an extension of the olderSweave/Latex environment. Rendering of mathematical expressions and referencemanagement is also supported by R Markdown using embedded Latex syntax andBibtex, respectively.

Quick Start

Install R Markdown

Initialize a new R Markdown (Rmd) script

R markdown latex cheat sheet

To minimize typing, it can be helful to start with an R Markdown template andthen modify it as needed. Note the file name of an R Markdown scirpt needs tohave the extension .Rmd. Template files for the following examples are availablehere:

  • R Markdown sample script: sample.Rmd
  • Bibtex file for handling citations and reference section: bibtex.bib

Users want to download these files, open the sample.Rmd file with their preferred R IDE(e.g. RStudio, vim or emacs), initilize an R session and then direct their R session tothe location of these two files.

Metadata section

The metadata section (YAML header) in an R Markdown script defines how it will be processed andrendered. The metadata section also includes both title, author, and date information as well asoptions for customizing the output format. For instance, PDF and HTML output can be definedwith pdf_document and html_document, respectively. The BiocStyle:: prefix will use theformatting style of the BiocStylepackage from Bioconductor.

Render Rmd script

An R Markdown script can be evaluated and rendered with the following render command or by pressing the knit button in RStudio.The output_format argument defines the format of the output (e.g.html_document). The setting output_format='all' will generateall supported output formats. Alternatively, one can specify several output formats in the metadata section as shown in the above example.

Cheat

The following shows two options how to run the rendering from the command-line.

Alternatively, one can use a Makefile to evaluate and render an R Markdownscript. A sample Makefile for rendering the above sample.Rmd can bedownloaded here.To apply it to a custom Rmd file, one needs open the Makefile in a texteditor and change the value assigned to MAIN (line 13) to the base name ofthe corresponding .Rmd file (e.g. assign systemPipeRNAseq if the filename is systemPipeRNAseq.Rmd). To execute the Makefile, run the followingcommand from the command-line.

R code chunks

R Code Chunks can be embedded in an R Markdown script by using three backticksat the beginning of a new line along with arguments enclosed in curly bracescontrolling the behavior of the code. The following lines contain theplain R code. A code chunk is terminated by a new line starting with three backticks.The following shows an example of such a code chunk. Note the backslashes arenot part of it. They have been added to print the code chunk syntax in this document.

The following lists the most important arguments to control the behavior of R code chunks:

  • r: specifies language for code chunk, here R
  • chode_chunk_name: name of code chunk; this name needs to be unique
  • eval: if assigned TRUE the code will be evaluated
  • warning: if assigned FALSE warnings will not be shown
  • message: if assigned FALSE messages will not be shown
  • cache: if assigned TRUE results will be cached to reuse in future rendering instances
  • fig.height: allows to specify height of figures in inches
  • fig.width: allows to specify width of figures in inches

For more details on code chunk options see here.

Learning Markdown

The basic syntax of Markdown and derivatives like kramdown is extremely easy to learn. Ratherthan providing another introduction on this topic, here are some useful sites for learning Markdown:

Tables

Markdown

There are several ways to render tables. First, they can be printed within the R code chunks. Second,much nicer formatted tables can be generated with the functions kable, pander or xtable. The followingexample uses kable from the knitr package.

Sepal.LengthSepal.WidthPetal.LengthPetal.WidthSpecies
5.13.51.40.2setosa
4.93.01.40.2setosa
4.73.21.30.2setosa
4.63.11.50.2setosa
5.03.61.40.2setosa
5.43.91.70.4setosa
4.63.41.40.3setosa
5.03.41.50.2setosa
4.42.91.40.2setosa
4.93.11.50.1setosa
5.43.71.50.2setosa
4.83.41.60.2setosa

A much more elegant and powerful solution is to create fully interactive tables with the DT package.This JavaScirpt based environment provides a wrapper to the DataTables library using jQuery. The resulting tables can be sorted, queried and resized by theuser.

Figures

Plots generated by the R code chunks in an R Markdown document can be automaticallyinserted in the output file. The size of the figure can be controlled with the fig.heightand fig.width arguments.

Cheat Sheet R Markdown

Sometimes it can be useful to explicitly write an image to a file and then insert thatimage into the final document by referencing its file name in the R Markdown source. Forinstance, this can be useful for time consuming analyses. The following code will generate afile named myplot.png. To insert the file in the final document, one can use standardMarkdown or HTML syntax, e.g.: <img src='myplot.png'/>.

Inline R code

To evaluate R code inline, one can enclose an R expression with a single back-tickfollowed by r and then the actual expression. For instance, the back-ticked versionof ‘r 1 + 1’ evaluates to 2 and ‘r pi’ evaluates to 3.1415927.

Mathematical equations

To render mathematical equations, one can use standard Latex syntax. When expressions areenclosed with single $ signs then they will be shown inline, whileenclosing them with double $$ signs will show them in display mode. For instance, the followingLatex syntax d(X,Y) = sqrt[]{ sum_{i=1}^{n}{(x_{i}-y_{i})^2} } renders in display mode as follows:

Sheet

$$d(X,Y) = sqrt[]{ sum_{i=1}^{n}{(x_{i}-y_{i})^2} }$$

Citations and bibliographies

Citations and bibliographies can be autogenerated in R Markdown in a similarway as in Latex/Bibtex. Reference collections should be stored in a separatefile in Bibtex or other supported formats. To cite a publication in an R Markdownscript, one uses the syntax [@<id1>] where <id1> needs to be replaced with areference identifier present in the Bibtex database listed in the metadata sectionof the R Markdown script (e.g.bibtex.bib). For instance, to cite Lawrence et al. (2013), one uses its reference identifier (e.g.Lawrence2013-kt) as <id1> (Lawrence et al. 2013).This will place the citation inline in the text and add the correspondingreference to a reference list at the end of the output document. For the latter aspecial section called References needs to be specified at the end of the R Markdown script.To fine control the formatting of citations and reference lists, users want to consult thisthe corresponding R Markdown page.Also, for general reference management and outputting references in Bibtex format Paperpilecan be very helpful.

Viewing R Markdown report on HPCC cluster

R Markdown reports located on UCR’s HPCC Cluster can be viewed locally in a web browser (without movingthe source HTML) by creating a symbolic link from a user’s .html directory. This way any updates tothe report will show up immediately without creating another copy of the HTML file. For instance, if userttest has generated an R Markdown report under ~/bigdata/today/rmarkdown/sample.html, then thesymbolic link can be created as follows:

After this one can view the report in a web browser using this URL http://biocluster.ucr.edu/~ttest/rmarkdown/sample.html.If necessary access to the URL can be restricted with a password following the instructions here.

R Markdown Reference Guide

Lawrence, Michael, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin T Morgan, and Vincent J Carey. 2013. “Software for Computing and Annotating Genomic Ranges.” PLoS Comput. Biol. 9 (8): e1003118. https://doi.org/10.1371/journal.pcbi.1003118.