Reproducible reports with RMarkdown

class: center, middle, inverse, title-slide

.title[
# Reproducible reports with RMarkdown
]
.author[
### Mikhail Dozmorov
]
.institute[
### Virginia Commonwealth University
]
.date[
### 2025-08-20
]

---

<style>
.large { font-size: 130%; }
.small { font-size: 70%; }
.tiny { font-size: 40%; }
</style>

## 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.** Basic idea - use human- and computer-readable chunks.

--*Donald E. Knuth, Literate Programming, 1984*

---
class: center, middle

# RMarkdown/knitR

<!--
## Writing reports

- **HTML**: HyperText Markup Language, the standard markup for creating web pages. First version released in 1993.

- **LaTeX**: a high-quality typesetting system for technical/scientific documentation (especially math-heavy). Primarily outputs PDF. First released in 1984 (Leslie Lamport’s LaTeX 2.09), with roots in TeX (1978).

- **Sweave**: integrates R code into LaTeX documents for reproducible PDF reports. Introduced in 2002.

- **Markdown**: a lightweight markup language for plain text formatting. Introduced in 2004. Easily converted to HTML, PDF, Word, and more.

- **Quarto**: a modern, open-source publishing system (successor to R Markdown) for creating documents, presentations, dashboards, and websites from R, Python, Julia, or Observable JavaScript. Supports HTML, PDF, Word, and more.

## HTML Example

- HTML files have the `.html` extension.
- Content and formatting are defined by **tags** (usually in opening/closing pairs).
- Tags can be **nested** to combine structure and style.

``` html
<!DOCTYPE html>
<html>
  <head>
    <title>My First Webpage</title>
  </head>
  <body>
    <h1>Header Level 1</h1>
    <p>This is a <strong>paragraph</strong> with <em>emphasized text</em>.</p>
    <p>Here is a link to <a href="https://www.example.com">Example.com</a>.</p>
    <ul>
      <li>First bullet item</li>
      <li>Second bullet item</li>
    </ul>
  </body>
</html>
```

## LaTeX Example

- LaTeX files usually have the `.tex` extension.  
- Commands begin with a backslash (`\`) and define appearance, structure, or formatting.  
- Environments (e.g., `\\begin{...}...\\end{...}`) wrap larger structures like equations, tables, or lists.

``` latex
\documentclass{article}

\begin{document}

\section{Introduction}
This is a simple \LaTeX{} document.  
We can write text, include \textbf{bold} or \emph{italic} formatting,  
and add mathematical formulas like $ E = mc^2 $.

\subsection{A List}
\begin{itemize}
  \item First bullet point
  \item Second bullet point
\end{itemize}

```

## Sweave example

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

``` sweave
\documentclass{article}
\usepackage{amsmath}

\begin{document}
We start by loading a built-in dataset:

<<load-data, echo=TRUE>>=
data(mtcars)
summary(mtcars$mpg)
@

The average MPG is \Sexpr{round(mean(mtcars$mpg), 1)}.

<<mpg-plot, fig=TRUE, echo=TRUE>>=
hist(mtcars$mpg, main = "Miles per Gallon",
     xlab = "MPG", col = "lightblue")
@

\end{document}
```
-->

---
## Markdown syntax

`*italic*` &nbsp; OR &nbsp; `_italic_` &nbsp;&nbsp;&nbsp; _italics_

`**bold**` &nbsp; OR &nbsp;  `__bold__` &nbsp;&nbsp;&nbsp; __bold__

**Headers**

`# Header 1`

`## Header 2`

`### Header 3`

---
## Markdown syntax | Lists

**Unordered List**

`* Item 1`

`* Item 2`

&nbsp;&nbsp;&nbsp; ` [TAB][TAB] * Item 2a`

(To achieve a subpoint, tab twice)

---
## Markdown syntax | Lists

**Ordered List**

`1. Item 1`

`2. Item 2`

`3. Item 3`

&nbsp;&nbsp;&nbsp; ` [TAB][TAB] + Item 3a`

&nbsp;&nbsp;&nbsp; ` [TAB][TAB] + Item 3b`

---
## Markdown syntax

`superscript^2^` &nbsp;&nbsp;&nbsp; x^2^

`~~strikethrough~~` &nbsp;&nbsp;&nbsp; ~~powerpoint~~

**Horizontal Rule / Page Break**

`******`

`------`

**Blockquotes**

A friend once said:

`> It's always better to give`  
`> than to receive.`

---
## Markdown syntax

**Links**

`http://example.com`

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

**Images**

`![](http://example.com/logo.png)`

`![optional caption text](figures/img.png)`

`<center><img src="img/clustering.png" height="370px" /></center>`

`knitr::include_graphics("img/knitr.png")`

---
## Markdown syntax

**Tables**

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

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

http://www.tablesgenerator.com/markdown_tables

---
## Creating R markdown document

- R Markdown files have .Rmd extension and combine text, code, and output
- In RStudio: File → New File → R Markdown
- Choose document type (HTML, PDF, Word) and fill in title/author
- RStudio provides a template with examples to get you started

---
## Creating R markdown document

---
## Mix and match HTML & LaTeX

R Markdown allows you to combine **Markdown** syntax with **HTML** and **LaTeX** for advanced formatting.

#### Inline HTML:
`<span style="color:blue;">Change text color</span>`  
<span style="color:blue;">Change text color</span>

`<center>Centered text or images</center>`
<center>Centered text or images</center>

#### Inline LaTeX:
`$\alpha + \beta = \gamma$` → renders as α + β = γ

---
## YAML header (think settings)

- YAML: YAML Ain't Markup Language (recursive acronim)
- YAML is a simple text-based format for specifying data, like JSON

``` yml
---
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`

Comments `#` allowed - create a very detailed YAML header and comment out what's not needed

.small[ http://rmarkdown.rstudio.com/html_document_format.html ]

---
## R Markdown | Code embedding

- Chunks of code are labeled in two ways:  
  - **Non-executable code formatting:** Single backticks around text like `myfunc()` renders in monospace font for display only
  - **Inline executable code:** Single backticks with `r` and a space, then your R code, then closing backtick. The `r` indicates executable R code that runs and shows results in real time.

Examples of inline code:

The estimated correlation is [backtick r cor(x, y) backtick]

Benefits: Instead of hard coding numbers, inline code automatically updates when data changes during knitting.  
*Note: Replace [backtick] with the actual backtick character when typing*

.small[ https://support.rstudio.com/hc/en-us/articles/205368677-R-Markdown-Dynamic-Documents-for-R ]

---
## Large code chunks

- Marked with [three backticks]{r chunk_name, options} followed by R code, then [three backticks] to close

Example structure:  
[three backticks]{r chunk_name, verbatim=TRUE, eval=FALSE}  
x = Inf + .Machine$xmin  
x  
[three backticks]

- The chunk nameis optional but helpful for organization
- By default, both the R code AND its output are displayed in the report
- Options like eval=FALSE control whether code runs, echo=FALSE hides code but shows output

Note: Replace [three backticks] with actual backtick characters when typing

---
## Chunk options (comma-separated)

- `echo=FALSE` *(default: TRUE)* — hide the code, show only output.

- `results='hide'` *(default: 'asis')* — hide output. `'hold'` delays output until the end of the chunk.

- `eval=FALSE` *(default: TRUE)* — display code without running it.

- `cache=TRUE` *(default: FALSE)* — cache results for slow computations.

- `fig.width=##`, `fig.height=##`, `fig.align="center"` — control figure size and alignment.

##### Example

\{r fig.width=5, fig.height=4, fig.align='center', echo=FALSE, cache=TRUE\}

---
## Global chunk options

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

&nbsp;

``` r
knitr::opts_chunk$set(fig.width=12, fig.height=8, fig.path='Figs/', 
                      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='Figs/'` the figure files get placed in the Figs subdirectory. (Default: not saved at all)

---
## Tables with `knitr::kable()`

- `knitr` has a built-in function to display a table quickly.

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

|                  |  mpg| cyl| disp|  hp| drat|    wt|  qsec| vs| am| gear| carb|
|:-----------------|----:|---:|----:|---:|----:|-----:|-----:|--:|--:|----:|----:|
|Mazda RX4         | 21.0|   6|  160| 110| 3.90| 2.620| 16.46|  0|  1|    4|    4|
|Mazda RX4 Wag     | 21.0|   6|  160| 110| 3.90| 2.875| 17.02|  0|  1|    4|    4|
|Datsun 710        | 22.8|   4|  108|  93| 3.85| 2.320| 18.61|  1|  1|    4|    1|
|Hornet 4 Drive    | 21.4|   6|  258| 110| 3.08| 3.215| 19.44|  1|  0|    3|    1|
|Hornet Sportabout | 18.7|   8|  360| 175| 3.15| 3.440| 17.02|  0|  0|    3|    2|
|Valiant           | 18.1|   6|  225| 105| 2.76| 3.460| 20.22|  1|  0|    3|    1|

---
## Tables with pander::pander()

- `pander` package offers more customization for plain-text and markdown tables.

``` r
library(pander)
panderOptions('table.style', 'rmarkdown') 
panderOptions('table.split.table', Inf)
pander(head(mtcars))
```

|        &nbsp;         | mpg  | cyl | disp | hp  | drat |  wt   | qsec  | vs | am | gear | carb |
|:---------------------:|:----:|:---:|:----:|:---:|:----:|:-----:|:-----:|:--:|:--:|:----:|:----:|
|     **Mazda RX4**     |  21  |  6  | 160  | 110 | 3.9  | 2.62  | 16.46 | 0  | 1  |  4   |  4   |
|   **Mazda RX4 Wag**   |  21  |  6  | 160  | 110 | 3.9  | 2.875 | 17.02 | 0  | 1  |  4   |  4   |
|    **Datsun 710**     | 22.8 |  4  | 108  | 93  | 3.85 | 2.32  | 18.61 | 1  | 1  |  4   |  1   |
|  **Hornet 4 Drive**   | 21.4 |  6  | 258  | 110 | 3.08 | 3.215 | 19.44 | 1  | 0  |  3   |  1   |
| **Hornet Sportabout** | 18.7 |  8  | 360  | 175 | 3.15 | 3.44  | 17.02 | 0  | 0  |  3   |  2   |
|      **Valiant**      | 18.1 |  6  | 225  | 105 | 2.76 | 3.46  | 20.22 | 1  | 0  |  3   |  1   |

---
## Tables with xtable::xtable()

- `xtable` converts R data frames to LaTeX or HTML tables, allowing fine formatting control.

``` r
library(xtable)
print(xtable(head(mtcars)), type = "html")
```

<table border=1>
<tr> <th>  </th> <th> mpg </th> <th> cyl </th> <th> disp </th> <th> hp </th> <th> drat </th> <th> wt </th> <th> qsec </th> <th> vs </th> <th> am </th> <th> gear </th> <th> carb </th>  </tr>
  <tr> <td align="right"> Mazda RX4 </td> <td align="right"> 21.00 </td> <td align="right"> 6.00 </td> <td align="right"> 160.00 </td> <td align="right"> 110.00 </td> <td align="right"> 3.90 </td> <td align="right"> 2.62 </td> <td align="right"> 16.46 </td> <td align="right"> 0.00 </td> <td align="right"> 1.00 </td> <td align="right"> 4.00 </td> <td align="right"> 4.00 </td> </tr>
  <tr> <td align="right"> Mazda RX4 Wag </td> <td align="right"> 21.00 </td> <td align="right"> 6.00 </td> <td align="right"> 160.00 </td> <td align="right"> 110.00 </td> <td align="right"> 3.90 </td> <td align="right"> 2.88 </td> <td align="right"> 17.02 </td> <td align="right"> 0.00 </td> <td align="right"> 1.00 </td> <td align="right"> 4.00 </td> <td align="right"> 4.00 </td> </tr>
  <tr> <td align="right"> Datsun 710 </td> <td align="right"> 22.80 </td> <td align="right"> 4.00 </td> <td align="right"> 108.00 </td> <td align="right"> 93.00 </td> <td align="right"> 3.85 </td> <td align="right"> 2.32 </td> <td align="right"> 18.61 </td> <td align="right"> 1.00 </td> <td align="right"> 1.00 </td> <td align="right"> 4.00 </td> <td align="right"> 1.00 </td> </tr>
  <tr> <td align="right"> Hornet 4 Drive </td> <td align="right"> 21.40 </td> <td align="right"> 6.00 </td> <td align="right"> 258.00 </td> <td align="right"> 110.00 </td> <td align="right"> 3.08 </td> <td align="right"> 3.21 </td> <td align="right"> 19.44 </td> <td align="right"> 1.00 </td> <td align="right"> 0.00 </td> <td align="right"> 3.00 </td> <td align="right"> 1.00 </td> </tr>
  <tr> <td align="right"> Hornet Sportabout </td> <td align="right"> 18.70 </td> <td align="right"> 8.00 </td> <td align="right"> 360.00 </td> <td align="right"> 175.00 </td> <td align="right"> 3.15 </td> <td align="right"> 3.44 </td> <td align="right"> 17.02 </td> <td align="right"> 0.00 </td> <td align="right"> 0.00 </td> <td align="right"> 3.00 </td> <td align="right"> 2.00 </td> </tr>
  <tr> <td align="right"> Valiant </td> <td align="right"> 18.10 </td> <td align="right"> 6.00 </td> <td align="right"> 225.00 </td> <td align="right"> 105.00 </td> <td align="right"> 2.76 </td> <td align="right"> 3.46 </td> <td align="right"> 20.22 </td> <td align="right"> 1.00 </td> <td align="right"> 0.00 </td> <td align="right"> 3.00 </td> <td align="right"> 1.00 </td> </tr>
   </table>

---
## Interactive tables with DT::datatable()

`DT` is an R interface to the DataTables JavaScript library for interactive tables.

``` r
library(DT)
datatable(mtcars)
```

<div class="datatables html-widget html-fill-item" id="htmlwidget-036b0ccf6432ba0e411f" style="width:100%;height:auto;"></div>
<script type="application/json" data-for="htmlwidget-036b0ccf6432ba0e411f">{"x":{"filter":"none","vertical":false,"data":[["Mazda RX4","Mazda RX4 Wag","Datsun 710","Hornet 4 Drive","Hornet Sportabout","Valiant","Duster 360","Merc 240D","Merc 230","Merc 280","Merc 280C","Merc 450SE","Merc 450SL","Merc 450SLC","Cadillac Fleetwood","Lincoln Continental","Chrysler Imperial","Fiat 128","Honda Civic","Toyota Corolla","Toyota Corona","Dodge Challenger","AMC Javelin","Camaro Z28","Pontiac Firebird","Fiat X1-9","Porsche 914-2","Lotus Europa","Ford Pantera L","Ferrari Dino","Maserati Bora","Volvo 142E"],[21,21,22.8,21.4,18.7,18.1,14.3,24.4,22.8,19.2,17.8,16.4,17.3,15.2,10.4,10.4,14.7,32.4,30.4,33.9,21.5,15.5,15.2,13.3,19.2,27.3,26,30.4,15.8,19.7,15,21.4],[6,6,4,6,8,6,8,4,4,6,6,8,8,8,8,8,8,4,4,4,4,8,8,8,8,4,4,4,8,6,8,4],[160,160,108,258,360,225,360,146.7,140.8,167.6,167.6,275.8,275.8,275.8,472,460,440,78.7,75.7,71.09999999999999,120.1,318,304,350,400,79,120.3,95.09999999999999,351,145,301,121],[110,110,93,110,175,105,245,62,95,123,123,180,180,180,205,215,230,66,52,65,97,150,150,245,175,66,91,113,264,175,335,109],[3.9,3.9,3.85,3.08,3.15,2.76,3.21,3.69,3.92,3.92,3.92,3.07,3.07,3.07,2.93,3,3.23,4.08,4.93,4.22,3.7,2.76,3.15,3.73,3.08,4.08,4.43,3.77,4.22,3.62,3.54,4.11],[2.62,2.875,2.32,3.215,3.44,3.46,3.57,3.19,3.15,3.44,3.44,4.07,3.73,3.78,5.25,5.424,5.345,2.2,1.615,1.835,2.465,3.52,3.435,3.84,3.845,1.935,2.14,1.513,3.17,2.77,3.57,2.78],[16.46,17.02,18.61,19.44,17.02,20.22,15.84,20,22.9,18.3,18.9,17.4,17.6,18,17.98,17.82,17.42,19.47,18.52,19.9,20.01,16.87,17.3,15.41,17.05,18.9,16.7,16.9,14.5,15.5,14.6,18.6],[0,0,1,1,0,1,0,1,1,1,1,0,0,0,0,0,0,1,1,1,1,0,0,0,0,1,0,1,0,0,0,1],[1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,0,0,0,0,1,1,1,1,1,1,1],[4,4,4,3,3,3,3,4,4,4,4,3,3,3,3,3,3,4,4,4,3,3,3,3,3,4,5,5,5,5,5,4],[4,4,1,1,2,1,4,2,2,4,4,3,3,3,4,4,4,1,2,1,1,2,2,4,2,1,2,2,4,6,8,2]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>mpg<\/th>\n      <th>cyl<\/th>\n      <th>disp<\/th>\n      <th>hp<\/th>\n      <th>drat<\/th>\n      <th>wt<\/th>\n      <th>qsec<\/th>\n      <th>vs<\/th>\n      <th>am<\/th>\n      <th>gear<\/th>\n      <th>carb<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[1,2,3,4,5,6,7,8,9,10,11]},{"orderable":false,"targets":0},{"name":" ","targets":0},{"name":"mpg","targets":1},{"name":"cyl","targets":2},{"name":"disp","targets":3},{"name":"hp","targets":4},{"name":"drat","targets":5},{"name":"wt","targets":6},{"name":"qsec","targets":7},{"name":"vs","targets":8},{"name":"am","targets":9},{"name":"gear","targets":10},{"name":"carb","targets":11}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>

---
## Creating the final report

- Markdown documents `*.md` 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 [http://pandoc.org/](http://pandoc.org/)

---
## Creating the final report: KnitR

- KnitR: a package for dynamic report generation written in R Markdown. PDF, HTML, DOCX output. Developed in 2012

- Available at: [https://github.com/yihui/knitr](https://github.com/yihui/knitr)

- Available for installation from CRAN, using:
`install.packages('knitr', dependencies = TRUE)`

---
## Creating the final report

- Rstudio: one button

- `knit2html()`, `knit2pdf`

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

---
## R Markdown best practices

- At the beginning, include a code chunk named `libraries`, and load all the packages in this chunk. Generally, it is good to load `dplyr` and `pander` packages by default.

- Include a `settings` code chunk, add any cutoff variables or boolean switches that control the behavior of the main code base. 
  - e.g. `pval_adj_cutoff <- 0.1 # Cutoff for FDR-adjusted filtering`
  - ~~An important settings affecting `data.frame` behavior to include is `stringsAsFactors = FALSE`~~
  - `set.seed(12345)`: initialize random number generator

---
## R Markdown best practices

- At the end of the document, include session information: outputs all packages/versions used

``` r
library("dplyr")
library("pander")
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$`*` == "*", ])
```

---
class: center, middle
# Bibliography

---
## 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}}
```
Save references in `.bib` text file

---
## BibTex managers

- **JabRef** (Windows, macOS, Linux) – http://www.jabref.org/
  - Open-source, cross-platform GUI for managing .bib files; integrates with LaTeX editors.
- **BibDesk** (macOS) – http://bibdesk.sourceforge.net/
  - Classic macOS BibTeX manager with citation search and integration into macOS services.
  - Tweaks for Pandoc: https://github.com/dsanson/bibdesk-pandoc-export-templates
- **Zotero** (Windows, macOS, Linux) – https://www.zotero.org/
  - Popular reference manager that can export .bib files; supports browser capture and plugins.
- **Mendeley Reference Manager** (Windows, macOS, Linux) – https://www.mendeley.com/
  - Cloud-based tool for organizing references and exporting to BibTeX.
  
---
## BibTex and RMarkdown

Add to YAML header

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

Insert into RMarkdown as

```
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

To apply a journal-specific citation style in R Markdown, add the following line to your YAML header:

```
csl: genomebiology.csl
```

- **CSL** (Citation Style Language) files define how references are formatted.

- You can download thousands of styles (e.g., APA, Nature, Genome Biology) from the Zotero Style Repository. https://www.zotero.org/styles

- Place the `.csl` file in your project directory so R Markdown can find it.

---
## Format your Word output

- When knitting to Word (.docx), you can customize fonts, headings, margins, and other styles instead of using the defaults.
  1. Create a template Word document with your preferred formatting.
    - Open a blank Word file, adjust styles (e.g., "Normal", "Heading 1") by right-clicking the style name and selecting Modify.
    - Save the file (e.g., `style.docx`).

- Reference the template in your YAML header:

```
output:
  word_document:
    reference_docx: style.docx
```

Your knitted Word file will use the styles from your template.

---
## Putting it all together

A complete YAML header example that combines **Word styling**, **bibliography references**, and **citation formatting** in one place:

```
---
title: "NIH Grant Proposal"
author: "Mikhail Dozmorov"
date: "2025-08-20"
output:
  word_document:
    reference_docx: styles/NIH_grant_style.docx
bibliography: references.bib
csl: bioinformatics.csl
link-citations: true
---
```

---
## RStudio "Visual" Mode

- Provides a **WYSIWYG** (What You See Is What You Get) editor for Markdown  
- Lets you apply **formatting visually** (bold, italic, headings, lists, tables) without typing syntax  
- Supports **inserting images, links, citations** via menus and dialogs  
- Switch easily between **Visual** and **Source** modes  
- Useful for beginners who want to focus on **content and style** rather than Markdown syntax  
- Still produces **plain-text Markdown** under the hood → fully compatible