Loadface346

• R Markdown Table Syntax
• R Markdown Table Syntax
• R Markdown Formula Syntax

Pycharm - Markdown syntax for table in Jupyter PyCharm pycharm. You can apply character formatting to a range of inline text with the following Markdown syntax. SourceForge uses markdown syntax everywhere to allow you to create rich. Text markup, and extends markdown in several ways to allow for quick linking.

Here is a brief introduction to using R Markdown.Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents and much, much more.R Markdown provides the flexibility of Markdown with the implementation of R input and output. For more details on using R Markdown see http://rmarkdown.rstudio.com.

1.1 Basic markdown syntax

1. Posted bymaelle-not-admin2020-07-03Posted incategory1, category2Tags: goodpress, R Markdown, WordPress. Formatting syntax for authoring HTML.
2. .::htmlvignette output engine by prettydoc::htmlpretty in your R Markdown header, and use one of the built-in themes and syntax highlighters.

1.1.1 Whitespace

Be careful with your spacing.While whitespace largely is ignored, it does at times give markdown signals as to how to proceed.As a habit, try to keep everything left aligned whenever possible, especially as you type a new paragraph.In other words, there is no need to indent basic text in the Rmd document (in fact, it might cause your text to do funny things if you do).

1.1.2 Italics and bold

• Italics are done like *this* or _this_
• Bold is done like **this** or __this__
• Bold and italics is done like ***this***, ___this___, or (the most transparent solution, in my opinion) **_this_**

1.1.3 Inline code

• Inline code is created with backticks like `this`

1.1.4 Sub and superscript

Sub₂ and super² script is created like this~2~ and this^2^

1.1.5 Strikethrough

• Strikethrough is done ~~like this~~

1.1.6 ‘Escaping’ (aka “What if I need an actual asterisk?”)

• To include an actual *, _ or , add another in front of them: *, _,

1.1.7 Endash (–), emdash (—)

• – and — with -- and ---

1.1.8 Blockquotes

Do like this:

Put a > in front of the line.

1.1.9 Headings

Section headers are created with #’s of increasing number, i.e.

• # First-level heading
• ## Second-level heading
• ### Etc.

R Markdown Table Syntax

In PDF output, a level-five heading will turn into a paragraph heading, i.e. paragraph{My level-five heading}, which appears as bold text on the same line as the subsequent paragraph.

1.1.10 Lists

Unordered list by starting a line with an * or a -:

• Item 1
• Item 2

Ordered lists by starting a line with a number.Notice that you can mislabel the numbers and Markdown will still make the order right in the output:

1. Item 1
2. Item 2

To create a sublist, indent the values a bit (at least four spaces or a tab):

1. Item 1
2. Item 2
3. Item 3
   • Item 3a
   • Item 3b

1.1.11 Line breaks

The official Markdown way to create line breaks is by ending a line with more than two spaces.

Roses are red.Violets are blue.

This appears on the same line in the output, because we didn’t add spaces after red.

Roses are red.
Violets are blue.

This appears with a line break because I added spaces after red.

I find this is confusing, so I recommend the alternative way: Ending a line with a backslash will also create a linebreak:

Roses are red.
Violets are blue.

To create a new paragraph, you put a blank line.

Therefore, this line starts its own paragraph.

1.1.12 Hyperlinks

• This is a hyperlink created by writing the text you want turned into a clickable link in [square brackets followed by a](https://hyperlink-in-parentheses)

1.1.13 Footnotes

• Are createdmy footnote text'>¹ by writing either ^[my footnote text] for supplying the footnote content inline, or something like [^a-random-footnote-label] and supplying the text elsewhere in the format shown below:This is a random test.'>²

[^a-random-footnote-label]: This is a random test.

1.1.15 Math

The syntax for writing math is stolen from LaTeX. To write a math expression that will be shown inline, enclose it in dollar signs.- This: $A = pi*r^{2}$ Becomes: (A = pi*r^{2})

To write a math expression that will be shown in a block, enclose it in two dollar signs.
This: $$A = pi*r^{2}$$

Becomes:[A = pi*r^{2}]

To create numbered equations, put them in an ‘equation’ environment and give them a label with the syntax (#eq:label), like this:

Becomes:[begin{equation}fleft(kright)=binom{n}{k}p^kleft(1-pright)^{n-k}tag{1.1}end{equation}]

For more (e.g. how to theorems), see e.g. the documentation on bookdown.org

1.2 Executable code chunks

The magic of R Markdown is that we can add executable code within our document to make it dynamic.

We do this either as code chunks (generally used for loading libraries and data, performing calculations, and adding images, plots, and tables), or inline code (generally used for dynamically reporting results within our text).

The syntax of a code chunk is shown in Figure 1.1.

Common chunk options include (see e.g. bookdown.org):

• echo: whether or not to display code in knitted output
• eval: whether or to to run the code in the chunk when knitting
• include: whether to include anything from the from a code chunk in the output document
• fig.cap: figure caption
• fig.scap: short figure caption, which will be used in the ‘List of Figures’ in the PDF front matter

IMPORTANT: Do not use underscoores in your chunk labels - if you do, you are likely to get an error in PDF output saying something like “! Package caption Error: caption outside float.”

1.2.1 Setup chunks - setup, images, plots

An R Markdown document usually begins with a chunk that is used to load libraries, and to set default chunk options with knitr::opts_chunk$set.

In your thesis, this will probably happen in index.Rmd and/or as opening chunks in each of your chapters.

1.2.2 Including images

Code chunks are also used for including images, with include_graphics from the knitr package, as in Figure 1.2

Figure 1.2: Oxford logo

Useful chunk options for figures include:

• out.width (use with a percentage) for setting the image size
• if you’ve got an image that gets waaay to big in your output, it will be constrained to the page width by setting out.width = '100%'

Figure rotation

You can use the chunk option out.extra to rotate images.

The syntax is different for LaTeX and HTML, so for ease we might start by assigning the right string to a variable that depends on the format you’re outputting to:

Then you can reference that variable as the value of out.extra to rotate images, as in Figure 1.3.

Figure 1.3: Oxford logo, rotated

1.2.3 Including plots

Similarly, code chunks are used for including dynamically generated plots.You use ordinary code in R or other languages - Figure 1.4 shows a plot of the cars dataset of stopping distances for cars at various speeds (this dataset is built in to R).

Figure 1.4: A ggplot of car stuff

Under the hood, plots are included in your document in the same way as images - when you build the book or knit a chapter, the plot is automatically generated from your code, saved as an image, then included into the output document.

1.2.4 Including tables

Tables are usually included with the kable function from the knitr package.

Table 1.1 shows the first rows of that cars data - read in your own data, then use this approach to automatically generate tables.

• Gotcha: when using kable, captions are set inside the kable function
• The kable package is often used with the kableExtra package

1.2.5 Control positioning

One thing that may be annoying is the way R Markdown handles “floats” like tables and figures.In your PDF output, LaTeX will try to find the best place to put your object based on the text around it and until you’re really, truly done writing you should just leave it where it lies.

In general, you should allow LaTeX to do this, but if you really really need a figure to be positioned where you put in the document, then you can make LaTeX attempt to do this with the chunk option fig.pos='H', as in Figure 1.5:

Figure 1.5: An Oxford logo that LaTeX will try to place at this position in the text

As anyone who has tried to manually play around with the placement of figures in a Word document knows, this can have lots of side effects with extra spacing on other pages, etc.Therefore, it is not generally a good idea to do this - only do it when you really need to ensure that an image follows directly under text where you refer to it (in this document, I needed to do this for Figure 3.1 in section 3.1.4).For more details, read the relevant section of the [R Markdown Cookbook]https://bookdown.org/yihui/rmarkdown-cookbook/figure-placement.html).

1.3 Executable inline code

‘Inline code’ simply means inclusion of code inside text.The syntax for doing this is `r R_CODE`For example, `r 4 + 4` will output 8 in your text.

You will usually use this in parts of your thesis where you report results - read in data or results in a code chunk, store things you want to report in a variable, then insert the value of that variable in your text.For example, we might assign the number of rows in the cars dataset to a variable:

We might then write:
“In the cars dataset, we have `r num_car_observations` observations.”

Which would output:
“In the cars dataset, we have 50 observations.”

1.4 Executable code in other languages than R

If you want to use other languages than R, such as Python, Julia C++, or SQL, see the relevant section of the R Markdown Cookbook

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

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.

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

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.

R Markdown Table Syntax

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.

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:

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

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 Formula Syntax

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.