Reproducible reports with Markdown, knitr, BibTex, MathJax

class: center, middle, inverse, title-slide

.title[
# Reproducible reports with Markdown, knitr, BibTex, MathJax
]
.author[
### Mikhail Dozmorov
]
.institute[
### Virginia Commonwealth University
]
.date[
### 09-06-2023
]

---

## Literate programming

Let us change our traditional attitude to the construction of programs: Instead of imagining that our main task is to instruct a computer what to do, **let us concentrate rather on explaining to humans what we want the computer to do.**

- Donald E. Knuth, Literate Programming, 1984

---
## Writing reports

- **HTML** - HyperText Markup Language, used to create web pages. Developed in 1993

- **LaTeX** - a typesetting system for production of technical/scientific documentation, PDF output. Developed in 1994

- **Sweave** - a tool that allows embedding of the R code in LaTeX documents, PDF output. Developed in 2002

- **Markdown** - a lightweight markup language for plain text formatting syntax. Easily converted to HTML, PDF, Word, and other formats

---
## HTML example

- HTML files have `.htm` or `.html` extensions
- Pairs of tags define content/formatting
    - `<h1> Header level 1 </h1>`
    - `<a href="http://www..."> Link </a>`
    - `<p> Paragraph </p>`

.small[
``` html
<!DOCTYPE html>
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
</head>

<body>
<h1>Markdown example</h1>

<p>This is a simple example of a Markdown document.</p>

You can emphasize code with <strong>bold</strong> or <em>italics</em>, or <code>monospace</code> font.
</body>
</html>
```
]

---
## LaTeX example

- LaTeX files usually have a `.tex` extension
- LaTeX commands define appearance of text, and other formatting structures

.small[
``` latex
\documentclass{article}
\usepackage{graphicx}

\begin{document}

\title{Introduction to \LaTeX{}}
\author{Author's Name}

\maketitle

\begin{abstract}
This is abstract text: This simple document shows very basic features of
\LaTeX{}.
\end{abstract}

\section{Introduction}
```
]
.small[ http://www.electronics.oulu.fi/latex/examples/example_1/ ]

---
## Sweave example

- Sweave files typically have an `.Rnw` extension
- LaTeX for text, `<<chunk_name>>= <code> @` syntax outlines code blocks

.small[
``` latex
\documentclass{article}

\usepackage{amsmath}

\DeclareMathOperator{\logit}{logit}

% \VignetteIndexEntry{Logit-Normal GLMM Examples}

\begin{document}

First we attach the data.
<<gapminder>>=
library(dslabs)
data(gapminder)
attach(gapminder)
@
```
]

---
## Markdown

- Lightweight markup language.
- Uses plain text.
- Simple, human-readable syntax.
- Used for formatting documents, including slides.
- Popular among programmers and writers.
- Easily converted to presentation format.
- Simplifies content creation and editing.

---
## R Markdown

- R Markdown is a Markdown markup language extended with the ability to add R code.
- The goal is still to separate form and content, but also to prioritize human-readability, even at the cost of fancy features
- You can learn Markdown in about 5 minutes. If you can write an email, you can write Markdown. See "Help -> Markdown Quick Reference" (also, "Cheatsheets")
- Can be converted in various document types, including HTML, PDF, MS Word, Beamer, HTML5 slides, Tufte-style handouts, books, dashboards, shiny applications, scientific articles, websites, and more.
- Fully supported in RStudio. Or, use a desktop Markdown editor like `MarkdownPad` (Windows) or `MacDown` (Mac).

.small[ http://bioconnector.github.io/markdown - Markdown Reference

http://markdownpad.com/ - a full-featured Markdown editor for Windows

http://macdown.uranusjr.com/ - the open source Markdown editor for macOS ]

---
## Basic Markdown Syntax

Regardless of your chosen output format, some basic syntax will be useful:

- Section headers
 
 - Text emphasis
 
 - Lists
 
 - `R` code
 
---
## Section Headers

To set up different sized header text in your document, use `#` for Header 1, `##` for Header 2, and `###` for Header 3.

``` rmarkdown
# Table of content
## Chapter 1
### Introduction
```

Renders as

# Table of content  
## Chapter 1  
### Introduction

---
## Text emphasis

- *Italicize* text via `*Italicize*` or `_Italicize_`
 
 - **Bold** text via `**Bold**` or `__Bold__`

---
## Unordered Lists

This code

``` text
- Item 1
- Item 2
    + Item 2a
    + Item 2b
```

Renders these bullets (sub-lists need 1 tab or 4 spaces!)

- Item 1
- Item 2
    + Item 2a
    + Item 2b

---
## Ordered Lists

This code

``` text
1. Item 1
2. Item 2
    + Item 2a
    + Item 2b
```

Renders this list (be advised - the bullets may not look great in all templates)

1. Item 1
2. Item 2
  + Item 2a
  + Item 2b

---
## Inline `R` Code

- To use `R` within a line, use the syntax, wrapped in single forward ticks (can't be displayed)

```
##      `r dim(mtx)`
```

- This can be useful to refer to estimates, confidence intervals, p-values, etc. in the body of an article/homework without worrying about copy errors.

---
## Markdown syntax

``` text
superscript^2^
~~strikethrough~~

Links
http://example.com
[linked phrase](http://example.com)

Images
![](http://example.com/logo.png)
![optional caption text](figures/img.png)
```

---
## Markdown syntax

``` text
Blockquotes
A friend once said:
> It's always better to give
> than to receive.

Horizontal Rule / Page Break
******
------

Tables

First Header  | Second Header
------------- | -------------
Content Cell  | Content Cell
Content Cell  | Content Cell
```

.small[ https://www.tablesgenerator.com/markdown_tables ]

---
## Large code chunks

Marked with triple backticks

```{r optionalChunkName, echo=TRUE, results='hide'} 
     # R code here 
     ```

- `Command+Option+I` (`Ctrl+Alt+I` on Windows) inserts R code chunk
- `Insert` button

---
## Creating R markdown document

.pull-left[
- Regular text file with `.Rmd` extension

- Create manually, or use RStudio

- "File -> New File" menu provides options for creating various R documents

]

.pull-right[<img src="img/create_rmarkdown.png" height=450 > ]

---
## R Markdown formats from RStudio

- **Documents**: HTML, PDF, Word, ODT, RTF

- **Presentations**: ioslides, beamer, reveal.js, Slidy, Xaringan, PowerPoint

- **Journals**: template packages for major journals/publishers

- **Web sites**: bookdown, blogdown, pkgdown, flexdashboard, Shiny, GitHub document

.small[https://rmarkdown.rstudio.com/formats.html]

---
## YAML header (think settings)

- YAML - YAML Ain't Markup Language

- YAML is a simple text-based format for specifying data, like JSON

``` yaml
---
title: "Untitled"
author: ”Your Name"
date: ”Current date"
output: html_document
---
```

`output` is the critical part - it defines the output format. Can be `pdf_document` or `word_document`, other formats available

---
## YAML header for a PDF presentation

``` yaml
---
title: "Reproducible reports with Markdown, knitr"
author: "Mikhail Dozmorov"
date: "2023-09-06"
output:
  beamer_presentation:
    # colortheme: seahorse
    colortheme: dolphin
    fig_caption: no
    fig_height: 6
    fig_width: 7
    fonttheme: structurebold
    # theme: boxes
    theme: AnnArbor
---
```

---
## YAML header for a Word document

``` yaml
---
bibliography: [3D_refs.bib,brain.bib]
csl: styles.ref/genomebiology.csl
output:
  word_document:
    reference_docx: styles.doc/NIH_grant_style.docx
  pdf_document: default
  html_document: default
---
```

---
## Modifying the behavior of R code chunks

Chunk options, comma-separated

- `echo=FALSE` - hides the code, but not the results/output. Default: TRUE

- `eval=FALSE` - disables code execution. Default: TRUE

- `cache=TRUE` - turn on caching of calculation-intensive chunk. Default: FALSE

- `fig.width=##`, `fig.height=##` - customize the size of a figure generated by the code chunk

- `include`: (`TRUE` by default) if this is set to `FALSE` the R code is still evaluated, but neither the code nor the results are returned in the output document

---
## Modifying the behavior of R code chunks

- `results="hide"` - hides the results/output.
    - `markup` (the default) takes the result of the R evaluation and turns it into markdown that is rendered as usual, 
    - `hold` - will hold all the output pieces and push them to the end of a chunk. Useful if you're running commands that result in lots of little pieces of output in the same chunk
    - `hide` will hide results
    - `asis` writes the raw results from R directly into the document. Only really useful for tables

.small[ The full list of options: http://yihui.name/knitr/options/ ]

---
## Global chunk options

- Some options you would like to set globally, instead of typing them for each chunk

``` r
knitr::opts_chunk$set(fig.width=12, fig.height=8, fig.path='img/’, cache.path='cache/', cache=FALSE, echo=FALSE, warning=FALSE, message=FALSE)
```

- `warning=FALSE` and `message=FALSE` suppress any R warnings or messages from being included in the final document

- `fig.path='img/'` - the figure files get placed in the `img` subdirectory. (Default: not saved at all)

---
## Caching

- The `cache=` option is automatically set to `FALSE`. That is, every time you render the Rmd, all the R code is run again from scratch

- If you use `cache=TRUE`, for this chunk, knitr will save the results of the evaluation into a directory that you specify, e.g., `cache.path='cache/'`. When you re-render the document, `knitr` will first check if there are previously cached results under the cache directory before really evaluating the chunk
    - if cached results exist and this code chunk has not been changed since last run (use MD5 sum to verify), the cached results will be (lazy-) loaded, otherwise new cache will be built
    - if a cached chunk depends on other chunks (see the `dependson` option) and any one of these chunks has changed, this chunk must be forcibly updated (old cache will be purged)
    
.small[ [Documentation for caching](http://yihui.name/knitr/demo/cache/) ]

---
## An example of R Markdown document

.center[ <img src="img/rmarkdown_doc_example.png" height=500> ]

---
## KnitR

- `KnitR` - Elegant, flexible, and fast dynamic report generation written in R Markdown. PDF, HTML, DOCX output. Developed in 2012 by Yihui Xie

``` r
install.packages('knitr', dependencies = TRUE)
```

To render a pdf from R Markdown, you need to have a version of TeX installed on your computer. Like R, TeX is open source software. RStudio recommends the following installations by system:

For Macs: MacTeX
For PCs: MiKTeX
Links for installing both can be found at http://www.latex-project.org/ftp.html

.small[ https://github.com/yihui/knitr, http://yihui.name/knitr/]

---
## Displaying data as tables

- KnitR has built-in function to display a table

``` r
data(mtcars)
knitr::kable(head(mtcars))
```

- `pander` package allows more customization

``` r
pander::pander(head(mtcars))
```

---
## Displaying data as tables

- `xtable` package has even more options

``` r
xtable::xtable(head(mtcars))
```

- DT package, an R interface to the DataTables library

``` r
DT::datatable(mtcars)
```

.small[ http://bioconnector.github.io/markdown/#!rmarkdown.md#Printing_tables_nicely

https://cran.r-project.org/web/packages/xtable/vignettes/xtableGallery.pdf

https://cran.r-project.org/web/packages/kableExtra/vignettes/awesome_table_in_html.html ]

---
## Including figures

- Plots may be generated by R code and displayed in the output document
- Existing image files like `*.jpg`, `*.png`, may be inserted like:

``` text
![](http://example.com/logo.png)
![optional caption text](figures/img.png)
```

- Alternatively, use `knitr` capabilities:

``` r
{r, out.width = '300px', echo=FALSE}
knitr::include_graphics('img/bandThree2.png')
```

- For PDF output, use LaTeX syntax:

``` latex
\begin{center}
\includegraphics[height=170px]{img/bioinfo3.png}
\end{center}
```

---
## Customizing Figures

The `fig.cap` option allows you to specify the caption for the figure generated by a given chunk:

````r
```{r caption, fig.cap="I am the caption"}
plot(pressure)
```
````

The `fig.height` and `fig.width` options let you specify the dimensions of your plots:

````r
```{r caption, fig.height = 4, fig.width = 8}
plot(pressure)
```
````

---
## Creating the final report

- Markdown documents (`*.md` or `*.Rmd`) can be converted to HTML using `markdown::markdownToHTML('markdown_example.md', 'markdown_example.html')`

- Another option is to use `rmarkdown::render('markdown_example.md’)`.  At the backend it uses `pandoc` command line tool, installed with Rstudio

- Rstudio - one button. `knit2html()`, `knit2pdf()` functions

**Note**: `KnitR` compiles the document in an R environment separate from yours (think `Makefile`). Do not use `./Rprofile` file - it loads into your environment only.

.small[ http://pandoc.org/ ]

---
## Things to include in your final report

`set.seed(12345)` - initialize random number generator

Include `session_info()` at the end - outputs all packages/versions used

```{r sessionInfo} 
     diagnostics <- devtools::session_info() 
     platform <- data.frame(diagnostics$platform %>% unlist, stringsAsFactors = FALSE) 
     colnames(platform) <- c('description') 
     pander(platform) 
     packages <- as.data.frame(diagnostics$packages) 
     pander(packages[ packages$`*` == '*', ]) 
     ``` 
Alternatively
     ```{r sessionInfo} 
     xfun::session_info() 
     ```

---
## Making default RMarkdown document on your own

Altering the default Rmarkdown file each time you write a homework, report, or article would be a pain.

- Fortunately, you don't have to!

---
## Templates

You can create your own templates which set-up packages, fonts, default chunk options, etc.

- https://bookdown.org/yihui/rmarkdown/document-templates.html

- Some packages (e.g `rticles`) provide templates that meet journal requirements or provide other.
    - Journal of Statistical Software
    - The R Journal
    - Association for Computing Machinery
    - ACS publications (Journal of the American Chemical Society, Environmental Science & Technology)
    - Elsevier publications

.small[https://github.com/mdozmorov/MDtemplate]

---
## Parameters

You may also set parameters in your document's YAML header

``` yaml
---
output: html_document
params:
  date: "2017-11-02"
---
```

or pass new values with the `render` function.

- This creates a read-only list `params` containing the values declared

- e.g. `params$date` returns `2017-11-02`

---
class: center, middle

# Bibliography

---
## BibTex

``` bibtex
@article{Berkum:2010aa,
	Abstract = {The three-dimensional folding of chromosomes ...},
	Author = {van Berkum, Nynke L and Lieberman-Aiden, Erez and Williams, Louise and Imakaev, Maxim and Gnirke, Andreas and Mirny, Leonid A and Dekker, Job and Lander, Eric S},
	Date-Added = {2016-10-08 14:26:23 +0000},
	Date-Modified = {2016-10-08 14:26:23 +0000},
	Doi = {10.3791/1869},
	Journal = {J Vis Exp},
	Journal-Full = {Journal of visualized experiments : JoVE},
	Mesh = {Chromosome Positioning; Chromosomes; DNA; Genomics; Nucleic Acid Conformation},
	Number = {39},
	Pmc = {PMC3149993},
	Pmid = {20461051},
	Pst = {epublish},
	Title = {Hi-C: a method to study the three-dimensional architecture of genomes},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.3791/1869}}
```

---
## BibTex managers

- `JabRef` for Windows, http://www.jabref.org/

- `BibDesk` for Mac, http://bibdesk.sourceforge.net/
  - https://github.com/dsanson/bibdesk-pandoc-export-templates - for Dragging and Dropping Pandoc-Style Citations from BibDesk

Save references in `.bib` text file

---
## Convert anything to BibTex

- doi2bib - BibTex from DOI, arXiv, biorXiv. https://www.doi2bib.org/

- Google Scholar - "Cite" as BibTeX functionality, https://scholar.google.com/

- ZoteroBib - create a bibliography from a URL, ISBN, DOI, PMID, arXiv ID, or title. Download as BibTex and more. https://zbib.org/

---
## BibTex and RMarkdown

Add to YAML header

``` yaml
bibliography: 3D_refs.bib
```

Insert into RMarkdown as

``` text
The 3D structure of the human genome has proven to be highly organized 
[@Dixon:2012aa; @Rao:2014aa]. This organization starts from distinct 
chromosome territories [@Cremer:2010aa], following by topologically associated 
domains (TADs) [@Dixon:2012aa; @Jackson:1998aa; @Ma:1998aa; @Nora:2012aa; @Sexton:2012aa], 
smaller "sub-TADs" [@Phillips-Cremins:2013aa; @Rao:2014aa] and, on the 
most local level, individual regions of interacting chromatin [@Rao:2014aa; @Dowen:2014aa; @Ji:2016aa].
```

---
## Format your BibTex references

Add to YAML header

``` yaml
csl: genomebiology.csl
```

Get more styles at https://www.zotero.org/styles

---
## Format your Word output

- If knitting into Word output, you may want to have fonts, headers, margins other than default.

- Create a Word document with the desired formatting. Change font styles by right-clicking on the font (e.g., "Normal") and select "Modify"

- Include it into YAML header

``` yaml
output:
  word_document:
    reference_docx: styles.doc/NIH_grant_style.docx
```

---
class: center, middle

# Math formulas

---
## Markdown Code: MathJax

- Markdown supports **MathJax JavaScript engine** to render mathematical equations and formulas
- Inline equations - use single "dollar sign" `$` to specify MathJax coding

``` text
$s^{2} = \frac{\sum(x-\bar{x})^2}{n-1}$
```

`$s^{2} = \frac{\sum(x-\bar{x})^2}{n-1}$`

.small[ Check out this online tutorial http://meta.math.stackexchange.com/questions/5020/mathjax-basic-tutorial-and-quick-reference

[MathJax_2.Rmd](https://github.com/ohsu-knight-cancer-biostatistics/reproducible-research/blob/32bba6a78e347d64745982fb6245915cecb1b7c3/slides-info-reproducible-research/study-group-2016/Chpt%2013%20Web%20Presentations/MathJax_2.Rmd) - Mathjax example ]
 
---
## Centering you equations

Insertion of two dollar signs `$$` centers your equations. Other examples, off set and centered - notice double dollar signs:
 
``` text
  $ \sum_{i=0}^n i^2 = \frac{(n^2+n)(2n+1)}{6} $
  
  $$ \sum_{i=0}^n i^2 = \frac{(n^2+n)(2n+1)}{6} $$
```

Inline equation  `$\sum_{i=0}^n i^2 = \frac{(n^2+n)(2n+1)}{6}$` on the same line. Or, self-standing equation on a separate line `$$\sum_{i=0}^n i^2 = \frac{(n^2+n)(2n+1)}{6}$$`
  
---
## More Interesting Codes:

**Greek Letters**
  
``` text
 $\alpha$      $\beta$       $\gamma$      $\chi$
 $\Delta$      $\Sigma$      $\Omega$
```

**Greek Letters:  (not all capitalized Greek letters available)**
  
`$\alpha$`      `$\beta$`       `$\gamma$`      `$\chi$`
 
`$\Delta$`      `$\Sigma$`      `$\Omega$`
  
**superscripts `(^)` and subscripts `(_)`**
  
`$x_i^2$`        `$log_2 x$`

---
## Grouping with Brackets

Use brackets {...} to delimit a formula containing a superscript or subscript.  Notice the difference the grouping makes:

``` text
${x^y}^z$
$x^{y^z}$ 
$x_i^2$
$x_{i^2}$
```
  
`${x^y}^z$`         `$x^{y^z}$` 
`$x_i^2$`           `$x_{i^2}$`

---
## Scaling:

Add the scaling code `\left(...\right)` to make automatic size adjustments

``` text
$(\frac{\sqrt x}{y^3})$
$\left(\frac{\sqrt x}{y^3}\right)$
```

`$(\frac{\sqrt x}{y^3})$`
`$\left(\frac{\sqrt x}{y^3}\right)$`

---
## Sums and Integrals

Subscript (_) designates the lower limit; superscript (^) designates upper limit:
 
``` text
$\sum_1^n$          $\sum_{i=0}^\infty i^2$
```

`$\sum_1^n$`          `$\sum_{i=0}^\infty i^2$`

Other notable symbols:
 
``` text
- $\prod$           $\infty$ 
- $\bigcup$         $\bigcap$
- $\int$            $\iint$
```

`$\prod$`              `$\infty$`
`$\bigcup$`            `$\bigcap$`
`$\int$`               `$\iint$`

---
## Radical Signs

Use 'sqrt' code to adjust the size of its argument. Note the change in size of the square root function based on the code

``` text
1. $sqrt{x^3}$
2. $sqrt[3]{\frac xy}$
 and for complicated expressions use  brackets
3. ${...}^{1/2}$
```

1. `$\sqrt{x^3}$`
2. `$\sqrt[3]{\frac xy}$`
3. `${...}^{1/2}$`

---
## You can also change fonts!

``` text
$\mathbb or $Bbb for 'Blackboard bold"
$\mathbf for boldface  
$\mathtt for 'typewritter' font
$\mathrm for roman font
$\mathsf for sans-serif
$\mathcal for 'caligraphy' 
$\mathscr for script letter: 
$\mathfrak for "Fraktur" (old German style)
```

`$\mathbb {ABCDEFG}$`   `$\mathbf {ABCDEFG}$`   `$\mathtt {ABCDEFG}$`   `$\mathrm {ABCDEFG}$`   `$\mathsf {ABCDEFG}$`   `$\mathcal {ABCDEFG}$`

---
## You can also change fonts!

Some special functions such as "lim" "sin" "max" and "ln" are normally set in roman font instead of italic.  Use `\lim`,  `\sin` to make these (roman):

``` text
$\sin x$   (roman)  vs  $sin x$  (italics)
```
`$\sin x$`   (roman)  vs `$sin x$`    (italics)

---
## And, add curly brackets

``` text
$$\begin{cases}
\widehat{IF_{1D}} = IF_{1D} - f(D)/2 \\
\widehat{IF_{2D}} = IF_{2D} + f(D)/2
\end{cases} \ (1)$$
```

`$$\begin{cases}
\widehat{IF_{1D}} = IF_{1D} - f(D)/2 \\
\widehat{IF_{2D}} = IF_{2D} + f(D)/2
\end{cases} \ (1)$$`

---
## RStudio bonus

Inline preview of forumlas and images in an RMarkdown document

.center[<img src="img/equation_preview_settings.png" height=380 >]

.small[ Preview online https://www.codecogs.com/latex/eqneditor.php]

---
## LaTeX and Markdown

- Rendering Markdown as a pdf requires a LaTeX installation
 
 - You will additionally need to install Pandoc from http://pandoc.org/
 
 - With LaTeX, many customizations are possible

---
## LaTeX Customization, 1

- You can include additional LaTeX commands and content

- Use the `includes` option as follows to add your favorite style files for the preamble, title/abstract, bibliography, etc...

``` yaml
---
title: 'A More Organized Person's Document'
output:
  beamer_presentation:
    includes:
      in_header: header.tex
      before_body: doc_prefix.tex
      after_body: doc_suffix.tex
---
```

---
## LaTeX Customization, 2

- If you prefer a self-contained document, you may opt for the `header-includes` option over the modular approach:

``` yaml
---
title: 'BIOS 691: Reproducible Research Tools'
author: "Author Name"
date: "November 2, 2017"
header-includes:
   - \usepackage{graphicx}
output: 
  beamer_presentation:
    theme: "Frankfurt"
---
```

---
## Quarto

Quarto is an open-source scientific and technical publishing system built on Pandoc.

- Python, R, Julia, and Observable support.
- Author documents as Markdown or Jupyter notebooks.
- Articles, reports, presentations, websites, blogs, and books in HTML, PDF, MS Word, ePub, and more.
- Supports scientific markdown, including equations, citations, crossrefs, figure panels, callouts, advanced layout, and more.
- Improved figure/table cross-referencing, labeling.

https://quarto.org/docs/get-started/

[Quarto - J.J. Allaire](https://youtu.be/9jGc0TxoRco) 1h video