Brief Instruction of Rmarkdown and Github

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# Brief Instruction of Rmarkdown and Github
### <br><br>Dr. Xiaotao Shen <br> Postdoctoral at <a href="http://snyderlab.stanford.edu/">Snyder lab</a> <br> <a href="http://shenxt.info"> <i class="fa fa-home fa-fw"></i>  shenxt.info</a><br> <a href="mailto:shenxt@stanford.edu"><i class="fa fa-paper-plane fa-fw"></i>  shenxt@stanford.edu</a><br>
### Stanford University School of Medicine
### 2020-03-17

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<div class="my-footer"><span>Xiaotao Shen/www.shenxt.info</span></div>

---

# Get started

.pull-left[

## The software we need

* git

* A github account

* R and Rmarkdown

* Typora
]

.pull-right[

## The R packages we need

* `rmarkdown`

* `blogdown`

* `tinytex`

* `xaringanthemer`

* `xaringan`

]

---

# Software

## git

Please download git and install it in your mac, PC or Linux. (https://git-scm.com/)

> Git is built in Mac and Linux. So you have no need to install it.

Open your terminal (Mac and Linux) or Git bash:

```markdown
git version
```

## Github

If you don't have a github accoiunt, please go to https://github.com/ and sign up.

---

# Software

## R and Rmarkdown

If you don't have R and Rmarkdown, please go https://www.r-project.org/ and https://rstudio.com/products/rstudio/download/, download and install them.

## Tytora

.pull-left[
Typora is a **markdown** editor.

Download it here https://typora.io/.
]

.pull-right[
<iframe height=250 width=300 src="figures/beta.mp4">
]

---

# R packages

Please open your Rstudio IDE and install the packages belows:

```r
install.packages("rmarkdown")
install.packages("blogdown")
install.packages("xaringan")
install.packages("xaringanthemer")
```

We also need LaTex, we can install it using `tinytext` in Rmarkdown:

```r
install.packages("tinytex")
tinytex::install_tinytex()  # install TinyTeX
```

Install `HUGO` using `blogdown` in Rstudio:

```r
blogdown::install_hugo()
```
---

# What is Markdown

.right-column[
- Markdown is a lightweight markup language with plain-text-formatting syntax.

- It's design allows it to be converted to many output formats. Such as HTML, PDF, word, PPT and so on.
]

.left-column[
<img src="figures/markdown_logo.png" style="width: 50%" />
]

---

# Syntax

.pull-left[

- Headers

- Lists

- Code blocks

- Links

- Emphasis

- Images
]

.pull-right[
- Highlighting

- Tables

- Blockquotes

- Horizontal line

- Equation

]

---

# Headers

.pull-left[
### Markdown

```r
# Heading level 1

## Heading level 2

### Heading level 3

#### Heading level 4

##### Heading level 5

###### Heading level 6
```
]

.pull-right[
### Rendered Output

# Heading level 1

## Heading level 2

### Heading level 3

#### Heading level 4

##### Heading level 5

###### Heading level 6

]

---

# Lists/ordered Lists

.pull-left[

### Markdown

```r
1. First item

2. Second item

3. Third item

4. Fourth item
```
]

.pull-right[

### Rendered Output

1. First item

2. Second item

3. Third item

4. Fourth item
]

---

# Lists/unordered Lists

.pull-left[

### Markdown

```r
- First item

- Second item

- Third item

- Indented item

- Fourth item
```
]

.pull-right[

### Rendered Output

- First item

- Second item

- Third item

- Indented item

- Fourth item
]

---

# Code blocks

.pull-left[

### Markdown

````markdown
```{r, eval=FALSE, echo=TRUE}
library(ggplot2)
library(tidyverse)
mtcars %>% 
ggplot(aes(x = gear, cyl)) + 
geom_point() + 
theme_bw()
```
````
]

.pull-right[

### Rendered Output

```r
library(ggplot2)
library(tidyverse)
mtcars %>% 
ggplot(aes(x = gear, cyl)) + 
geom_point() + 
theme_bw()
```
]

---

# Images/local

.pull-left[

### Markdown

```r
![Stanford University](stanford.png)
```
]

.pull-right[

### Rendered Output

![Stanford University](./stanford.png)

]

---

# Images/url

.pull-left[

### Markdown

```r
![Xiaotao Shen wechat](https://www.shenxt.info/files/wechat_QR.jpg)
```
]

.pull-right[

### Rendered Output

![Xiaotao Shen wechat](https://www.shenxt.info/files/wechat_QR.jpg)
]

---

# Emphasis

.pull-left[

### Markdown

````markdown
Markdown is a good tool.

**Markdown** is a good tool.

*Markdown* is a good tool.

***Markdown*** is a good tool.

````
]

.pull-right[

### Rendered Output

Markdown is a good tool.

**Markdown** is a good tool.

*Markdown* is a good tool.

***Markdown*** is a good tool.
]

---

# Tables

.pull-left[

### Markdown

```markdown
| First name    | Last name   | Sex  |
| ------------- |-------------| -----|
| Xiaotao       |Shen          | Male |
| Chuchu        | Wang      |   Female |

```
]

.pull-right[

### Rendered Output

| First name    | Last name   | Sex  |
| ------------- |-------------| -----|
| Xiaotao       |Shen          | Male |
| Chuchu        | Wang      |   Female |
]

---

# Blockquotes

.pull-left[

### Markdown

```markdown
> Blockquotes are very handy in email to emulate reply text.

> This line is part of the same quote.
```
]

.pull-right[

### Rendered Output

> Blockquotes are very handy in email to emulate reply text.

> This line is part of the same quote.

]

---

# Horizontal line

.pull-left[

### Markdown

```markdown

***

```
]

.pull-right[

### Rendered Output

This is a horizontal line.

***

]

---

# IDE of markddown

- <a href="http://note.youdao.com/" target="_blank" rel="noopener"><span>网易云笔记</span> </a>

- [Trpora](https://typora.io/)

- [Atom](https://atom.io/)

- [Rstudio](https://rstudio.com/)

- [Jupyper notebook](https://jupyter.org/)

---

# More information...

More information about `markdown`, `Rmarkdown`, `git&github` can be found here: https://jaspershen.github.io/r_cookbook/

The code of this Slides can be found here: https://github.com/jaspershen/current_topics_in_data_science_-and_omics