Hello Ninja

Xaringan is developed by Yihui Xie, the software engineer in RStudio.

You can install xaringan package from R CRAN or the latest version in Github

devtools::install_github("yihui/xaringan")

Hello Ninja

Xaringan is developed by Yihui Xie, the software engineer in RStudio.

You can install xaringan package from R CRAN or the latest version in Github

devtools::install_github("yihui/xaringan")

You are recommended to use the RStudio IDE, but you do not have to.

• Create a new R Markdown document from the menu File -> New File -> R Markdown -> From Template -> Ninja Presentation

Hello Ninja

Xaringan is developed by Yihui Xie, the software engineer in RStudio.

You can install xaringan package from R CRAN or the latest version in Github

devtools::install_github("yihui/xaringan")

You are recommended to use the RStudio IDE, but you do not have to.

• Create a new R Markdown document from the menu File -> New File -> R Markdown -> From Template -> Ninja Presentation

• Click the Knit button to compile it;

Hello Ninja

Xaringan is developed by Yihui Xie, the software engineer in RStudio.

You can install xaringan package from R CRAN or the latest version in Github

devtools::install_github("yihui/xaringan")

You are recommended to use the RStudio IDE, but you do not have to.

• Create a new R Markdown document from the menu File -> New File -> R Markdown -> From Template -> Ninja Presentation

• Click the Knit button to compile it;

• or use the RStudio Addin²; "Infinite Moon Reader" to live preview the slides (every time you update and save the Rmd document, the slides will be automatically reloaded in RStudio Viewer.

Why xaringan?

• Free and Open Source (Slides are composed in R Markdown)

• Version control

• Portable and easily share (Web-based slide)

• Easily print to PDF from Chrome

• Repoducibe research result

TAMU theme

The TAMU theme is based on Texas A&M University University Brand Guide. It consists of two CSS files. To use this template (the latest version), go to xaringan-tamu github repo and clone it. You only need to put your slide file (*.Rmd) and the template css (tamu.css, tamu-fonts.css) in the same folder.

Then, use it in the YAML metadata, e.g.:

---
title: "TAMU Presentation"
output:
  xaringan::moon_reader:
     css: ["default", "tamu.css", "tamu-fonts.css"]
    nature:
          highlightLines: true
---

TAMU theme

Not the GitHub User? No Problem!

Now, It's a built-in theme. Just simply revise the YAML:

---
output:
  xaringan::moon_reader:
     css: ["default", "tamu", "tamu-fonts"]
    nature:
          highlightLines: true
---

That's check some functions!

A FULL image

Look Good?

Foot note

Want to write the foot note? Embed the html script <sup>1</sup> like this¹:

.footnote[
[1] Y. Xie et al., xaringan: Presentation Ninja. 2018.
]

Also, this template was constructed refer to some examples^2,3,4

Font size

This is normal font size

Use .large[] to use large font

Use .small[] to use small font

Also, you can try this trick

Use .large[large[]] to use extra large font

Use .small[small[]] to use tiny font

Image size

Use .shrink[] to shrink the image

Image size

Use .enlarge[] to enlarge the image

Math Expressions

You can write LaTeX math expressions inside a pair of dollar signs. You can use the display style with double dollar signs. This is the Hill equation:

$$\theta=\frac{[L^n]}{k_d+[L]^n}$$

θ=[Ln]kd+[L]n

where

• θ is the fraction of the receptor protein concentration that is bound to ligand.
• [L] is the free (unbound) ligand concentration.
• kd is the apparent dissociation constant derived from the law of mass action (the equilibrium constant for dissociation).

R Code

# a boring regression
fit = lm(dist ~ 1 + speed, data = cars)
coef(summary(fit))

#               Estimate Std. Error   t value     Pr(>|t|)
# (Intercept) -17.579095  6.7584402 -2.601058 1.231882e-02
# speed         3.932409  0.4155128  9.463990 1.489836e-12

Use the quote? No problem!

"I came; I saw; I conquered"

dojutsu = c('VENI', 'VIDI', 'VICI')
grep('VI', dojutsu, value = TRUE)

## [1] "VIDI" "VICI"

R Plots

ggplot(NULL, aes(x = 1, y = 1)) +
  annotate("text", 1, 1, label = 'GiG\'EM AGGIES!', color = "#500000",
           fontface = "bold", size = 12)+
  theme(axis.title = element_blank(), axis.ticks = element_blank(),
           axis.text = element_blank())

Pharmacokinetics - Tables

If you want to generate a table, make sure it is in the HTML format (instead of Markdown or other formats), e.g.,

knitr::kable(head(MEMSS::Theoph), format = 'html')

DT::datatable(
  head(MEMSS::Theoph, 120),
  fillContainer = FALSE, options = list(pageLength = 7)
)

Pharmacokinetics - Plot

xyplot(conc ~ Time| Subject, data=Theoph, xlab="Time (hr)",
       auto.key = T,
       ylab=expression(paste("Plasma concentration, ",mu, "M")), type="b")

HTML Widgets - TAMU Map

library(leaflet)
leaflet() %>% addTiles() %>% setView(lng = -96.3570, lat = 30.6116, zoom = 12)

Highlight Lines

• The option highlightLines: true of nature will highlight code lines that start with *, or are wrapped in {{ }}, or have trailing comments #<<;

output:
  xaringan::moon_reader:
    nature:
    highlightLines: true

```{r tidy=FALSE}
if (TRUE) {
{{ message("Very important!") }}
}
```

if (TRUE) {
  message("Very important!") 
}

## Very important!