Demo Lab

RaukR 2023 • Advanced R for Bioinformatics

This is a demo quarto lab document to showcase the theme, style and usage.
Author

Roy Francis

Published

13-Jun-2023

1 Quarto & RMarkdown

  • This is a quarto document with RMarkdown.
  • Markdown basics are covered here.
  • In RStudio, you create a .qmd text file, then click the Render button.
  • .qmd documents can also be rendered as such:
quarto::quarto_render("report.qmd")

2 Layout

2.1 Inner columns

Organisation of content into columns within the body container.

:::: {.columns}
::: {.column style="background-color: aliceblue"}
Content is left.
:::
::: {.column style="background-color:  #f5b7b1"}
Content is right.
:::
::::

Content in left column.

Content in right column.


This is an example of nested columns.

:::: {.columns}

::: {.column style="background-color: aliceblue"}
Content in left column.
:::

::: {.column}
Content in right column.

:::: {.columns}
::: {.column style="background-color: #d0ece7"}
Nested left.
:::
::: {.column style="background-color: #f2d7d5"}
Nested right.
:::
::::

:::

::::

Content in left column.

Content in right column.

Nested left.

Nested right.

2.2 Outer columns

Extending content outside the body container.

::: {.column-body style="background-color: lightgray; margin-bottom:0.5em;"}
.column-body
:::

::: {.column-body-outset style="background-color: lightgray; margin-bottom:0.5em;"}
.column-body-outset
:::

::: {.column-page-inset style="background-color: lightgray; margin-bottom:0.5em;"}
.column-page-inset
:::

::: {.column-page style="background-color: lightgray; margin-bottom:0.5em;"}
.column-page
:::

::: {.column-screen-inset style="background-color: lightgray; margin-bottom:0.5em;"}
.column-screen-inset
:::

::: {.column-screen style="background-color: lightgray; margin-bottom:0.5em;"}
.column-screen
:::

::: {.column-body-outset-right style="background-color: lightgray; margin-bottom:0.5em;"}
.column-body-outset-right
:::

::: {.column-page-inset-right style="background-color: lightgray; margin-bottom:0.5em;"}
.column-page-inset-right
:::

::: {.column-page-right style="background-color: lightgray; margin-bottom:0.5em;"}
.column-page-right
:::

::: {.column-screen-inset-right style="background-color: lightgray; margin-bottom:0.5em;"}
.column-screen-inset-right
:::

::: {.column-screen-right style="background-color: lightgray; margin-bottom:0.5em;"}
.column-screen-right
:::

::: {.column-body-outset-left style="background-color: lightgray; margin-bottom:0.5em;"}
.column-body-outset-left
:::

::: {.column-page-inset-left style="background-color: lightgray; margin-bottom:0.5em;"}
.column-page-inset-left
:::

::: {.column-page-left style="background-color: lightgray; margin-bottom:0.5em;"}
.column-page-left
:::

::: {.column-screen-inset-left style="background-color: lightgray; margin-bottom:0.5em;"}
.column-screen-inset-left
:::

::: {.column-screen-left style="background-color: lightgray; margin-bottom:0.5em;"}
.column-screen-left
:::

::: {.column-margin style="background-color: lightgray; margin-bottom:0.5em;"}
.column-margin
:::

.column-body

.column-body-outset

.column-page-inset

.column-page

.column-screen-inset

.column-screen

.column-body-outset-right

.column-page-inset-right

.column-page-right

.column-screen-inset-right

.column-screen-right

.column-body-outset-left

.column-page-inset-left

.column-page-left

.column-screen-inset-left

.column-screen-left

.column-margin

2.3 Panel layout

::: {.panel-tabset}
#### Sub topic 1

This is some material for topic 1.

#### Sub topic 2

This is some material for topic 2.

:::

This is some material for topic 1.

This is some material for topic 2.

More layout settings are described here and here.

3 Text formatting

Headings can be defined as shown below.

## Level 2 heading  
### Level 3 heading  
#### Level 4 heading  
##### Level 5 heading  
###### Level 6 heading

3.1 Level 3 heading

3.1.1 Level 4 heading

Level 5 heading
Level 6 heading

Character styles can be set as below.

[Largest text]{.largest}  
[Larger text]{.larger}  
[Large text]{.large}  
Normal text  
[Small text]{.small}  
[Smaller text]{.smaller}  
[Smallest text]{.smallest}

Largest text
Larger text
Large text
Normal text
Small text
Smaller text
Smallest text

A horizontal line can be created using three or more * or -.

***

This is __Bold text__ This is Bold text
This is _Italic text_ This is Italic text
~~Strikethrough~~ text Strikethrough text
This is Subscript H~2~O displayed as H2O
This is Superscript 2^10^ displayed as 210
This is a [link](r-project.org) This is a link
An example of footnote reference 1

> This is a block quote. This
> paragraph has two lines.
>
> 1. This is a list inside a block quote.
> 2. Second item.

This is a block quote. This paragraph has two lines.

  1. This is a list inside a block quote.
  2. Second item.

[This content lives in the right margin]{.aside}

This content lives in the right margin

4 Code formatting

Code can be defined inline where `this` looks like this. R code can be executed inline `r Sys.Date()` producing 2023-06-12. Code can also be defined inside code blocks.

```


This is code
```

This is code

R code is executed inside code blocks like this

```{r}
Sys.Date()
```

which shows the code and output.

Sys.Date()
[1] "2023-06-12"

The code and results can be hidden while sill executing the code.

```{r}
#| eval: true
#| echo: false
#| results: hide
Sys.Date()
```

Here is another example of executed R code with input and output.

data(iris)
head(iris[,1:2])
Sepal.Length Sepal.Width
5.1 3.5
4.9 3.0
4.7 3.2
4.6 3.1
5.0 3.6
5.4 3.9

5 Lists

5.1 Bulleted List

Unordered lists are created using asterisks.

  • Bullet 1
  • Bullet 2
    • Sub-bullet 2.1
    • Sub-bullet 2.2
  • Bullet 3

Ordered lists are created using numbers.

  1. Point 1
  2. Point 2
  3. Point 3

6 Images

6.1 Using Markdown

Using regular markdown.

![](assets/featured.jpg)

The dimensions are based on image and/or fill up the entire available space. You can control the dimension as shown below.

![This is a caption](assets/featured.jpg){width=30%}

This is a caption

This image above is now 30% of it’s original width.

Figure layout.

::: {#fig1 layout-ncol=2}
![Caption for figure 1](assets/featured.jpg){#subfig1 width="40%"}

![Caption for figure 2](assets/featured.jpg){#subfig2 width="40%"}

These figures are interesting.
:::

Caption for figure 1

Caption for figure 2

These figures are interesting.

More figure options and layouts are described here. Cross referencing described here.

6.2 Using HTML

This image below is 30% size.
<img src="assets/featured.jpg" style="width:30%;"/>

6.3 Using R

R chunks in RMarkdown can be used to control image display size using the argument out.width.

This image below is displayed at a size of 300 pixels.

```{r}
#| out-width: 300px
knitr::include_graphics("assets/featured.jpg")
```

This image below is displayed at a size of 75 pixels and a caption added.

```{r}
#| out-width: 75px
#| fig-cap: This is a caption
knitr::include_graphics("assets/featured.jpg")
```

This is a caption

For more information on figures, see here. For plots generated through R, see section further below.

7 Math expressions

Some examples of rendering equations.

$e^{i\pi} + 1 = 0$

\(e^{i\pi} + 1 = 0\)

$$\frac{E \times X^2 \prod I}{2+7} = 432$$

\[\frac{E \times X^2 \prod I}{2+7} = 432\]

$$\sum_{i=1}^n X_i$$

\[\sum_{i=1}^n X_i\]

$$\int_0^{2\pi} \sin x~dx$$

\[\int_0^{2\pi} \sin x~dx\]

$\left( \sum_{i=1}^{n}{i} \right)^2 = \left( \frac{n(n-1)}{2}\right)^2 = \frac{n^2(n-1)^2}{4}$

\(\left( \sum_{i=1}^{n}{i} \right)^2 = \left( \frac{n(n-1)}{2}\right)^2 = \frac{n^2(n-1)^2}{4}\)

$\begin{eqnarray} X & \sim & \mathrm{N}(0,1)\\ Y & \sim & \chi^2_{n-p}\\ R & \equiv & X/Y \sim t_{n-p} \end{eqnarray}$

\(\begin{eqnarray} X & \sim & \mathrm{N}(0,1)\\ Y & \sim & \chi^2_{n-p}\\ R & \equiv & X/Y \sim t_{n-p} \end{eqnarray}\)

$\begin{eqnarray} P(|X-\mu| > k) & = & P(|X-\mu|^2 > k^2)\\ & \leq & \frac{\mathbb{E}\left[|X-\mu|^2\right]}{k^2}\\ & \leq & \frac{\mathrm{Var}[X]}{k^2} \end{eqnarray}$

\(\begin{eqnarray} P(|X-\mu| > k) & = & P(|X-\mu|^2 > k^2)\\ & \leq & \frac{\mathbb{E}\left[|X-\mu|^2\right]}{k^2}\\ & \leq & \frac{\mathrm{Var}[X]}{k^2} \end{eqnarray}\)

8 Tables

8.1 Manual

For simple cases, tables can be manually created in markdown.

|speed|dist|
|-----|----|
|4    |   2|
|4    |  10|
|7    |   4|
speed dist
4 2
4 10
7 4

8.2 htmlTable

Markdown tables can be enhanced using the R package htmlTable.

library(htmlTable)

iris1 <- iris[c(1:4,51:53,105:108),]
htmlTable(iris1, rgroup=unique(iris1$Species), n.rgroup=rle(as.character(iris1$Species))$lengths)
Sepal.Length Sepal.Width Petal.Length Petal.Width Species
setosa
  1 5.1 3.5 1.4 0.2 setosa
  2 4.9 3 1.4 0.2 setosa
  3 4.7 3.2 1.3 0.2 setosa
  4 4.6 3.1 1.5 0.2 setosa
versicolor
  51 7 3.2 4.7 1.4 versicolor
  52 6.4 3.2 4.5 1.5 versicolor
  53 6.9 3.1 4.9 1.5 versicolor
virginica
  105 6.5 3 5.8 2.2 virginica
  106 7.6 3 6.6 2.1 virginica
  107 4.9 2.5 4.5 1.7 virginica
  108 7.3 2.9 6.3 1.8 virginica

8.3 kable

Simple table using kable from R package knitr. This is the default output for quarto.

head(iris)
Sepal.Length Sepal.Width Petal.Length Petal.Width Species
5.1 3.5 1.4 0.2 setosa
4.9 3.0 1.4 0.2 setosa
4.7 3.2 1.3 0.2 setosa
4.6 3.1 1.5 0.2 setosa
5.0 3.6 1.4 0.2 setosa
5.4 3.9 1.7 0.4 setosa

8.3.1 Margin table

```{{r}}
#| fig-caption: This table is in the margin.
#| column: margin

head(cars)
```
speed dist
4 2
4 10
7 4
7 22
8 16
9 10

8.4 kableExtra

More advanced table using kableExtra and formattable.

library(kableExtra)

iris[c(1:4,51:53,105:108),] %>%
  mutate(Sepal.Length=color_bar("lightsteelblue")(Sepal.Length)) %>%
  mutate(Sepal.Width=color_tile("white","orange")(Sepal.Width)) %>%
  mutate(Species=cell_spec(Species,"html",color="white",bold=T,
    background=c("#8dd3c7","#fb8072","#bebada")[factor(.$Species)])) %>%
  kable("html",escape=F) %>%
  kable_styling(bootstrap_options=c("striped","hover","responsive"),
                full_width=F,position="left") %>%
  column_spec(5,width="3cm")
Table using kableextra.
Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1 5.1 3.5 1.4 0.2 setosa
2 4.9 3.0 1.4 0.2 setosa
3 4.7 3.2 1.3 0.2 setosa
4 4.6 3.1 1.5 0.2 setosa
51 7.0 3.2 4.7 1.4 versicolor
52 6.4 3.2 4.5 1.5 versicolor
53 6.9 3.1 4.9 1.5 versicolor
105 6.5 3.0 5.8 2.2 virginica
106 7.6 3.0 6.6 2.1 virginica
107 4.9 2.5 4.5 1.7 virginica
108 7.3 2.9 6.3 1.8 virginica

8.5 DT

Interactive table using R package DT.

library(DT)

iris %>%
  slice(1:15) %>%
  datatable(options=list(pageLength=7))

8.6 reactable

Advanced interactive tables with reactable.

library(reactable)

reactable(iris[sample(1:150,10),],
  columns = list(
    Sepal.Length = colDef(name = "Sepal Length"),
    Sepal.Width = colDef(name = "Sepal Width"),
    Petal.Width = colDef(name = "Petal Width"),
    Petal.Width = colDef(name = "Petal Width")
  ),
  striped = TRUE,
  highlight = TRUE,
  filterable = TRUE
)

reactable creation can be simplified as well as enhanced by using reactablefmtr.

9 Static plots

9.1 Base plot

  • Plots using base R are widely used and may be good enough for most situations.
  • But they lack a consistent coding framework.
{plot(x=iris$Sepal.Length,y=iris$Sepal.Width,
      col=c("coral","steelblue","forestgreen")[iris$Species],
      xlab="Sepal Length",ylab="Sepal Width",pch=19)
legend(x=7,y=4.47,legend=c("setosa","versicolor","virginica"),
       col=c("coral","steelblue","forestgreen"),pch=19)}

Static plot using base plot.

Refer to @plot-base to see an example of base plot.

9.1.1 Multiple plots

```{r}
#| column: screen-inset-shaded
#| layout-nrow: 1

plot(cars)
plot(iris)
plot(pressure)
```

9.1.2 Margin plot

```{{r}}
#| column: margin

plot(cars)
```
plot(cars)

9.2 ggplot2

R package ggplot2 is one of the most versatile and complete plotting solutions.

library(ggplot2)

iris %>%
  ggplot(aes(x=Sepal.Length,y=Sepal.Width,col=Species))+
  geom_point(size=2)+
  labs(x="Sepal Length",y="Sepal Width")+
  theme_report()

Static plot using ggplot2.

10 Interactive plots

10.1 rbokeh

R package rbokeh is an easy and convenient option to get started with interactive plots.

library(rbokeh)

figure(height=400,width=600,xlab="Sepal Length",ylab="Sepal Width") %>%
  ly_points(Sepal.Length,Sepal.Width,data=iris,
  color=Species,glyph=Species,hover=list(Sepal.Length,Sepal.Width))

Interactive scatterplot using rbokeh.

10.2 highcharter

R package highcharter is a wrapper around javascript library highcharts.

library(highcharter)

h <- iris %>%
  hchart(.,"scatter",hcaes(x="Sepal.Length",y="Sepal.Width",group="Species")) %>%
  hc_xAxis(title=list(text="Sepal Length"),crosshair=TRUE) %>%
  hc_yAxis(title=list(text="Sepal Width"),crosshair=TRUE) %>%
  hc_chart(zoomType="xy",inverted=FALSE) %>%
  hc_legend(verticalAlign="top",align="right") %>%
  hc_size(height=400)

htmltools::tagList(list(h))

Interactive scatterplot using highcharter.

10.3 plotly

R package plotly provides R binding around javascript plotting library plotly.

library(plotly)

p <- iris %>%
  plot_ly(x=~Sepal.Length,y=~Sepal.Width,color=~Species,width=500,height=400) %>%
  add_markers()
p

Interactive scatterplot using plotly.

10.4 ggplotly

plotly also has a function called ggplotly which converts a static ggplot2 object into an interactive plot.

library(plotly)

p <- iris %>%
  ggplot(aes(x=Sepal.Length,y=Sepal.Width,col=Species))+
  geom_point()+
  labs(x="Sepal Length",y="Sepal Width")+
  theme_bw(base_size=12)

ggplotly(p,width=500,height=400)

Interactive scatterplot using ggplotly.

10.5 ggiraph

ggiraph is also an R package that can be used to convert a static ggplot2 object into an interactive plot.

library(ggiraph)

p <- ggplot(iris,aes(x=Sepal.Length,y=Petal.Length,colour=Species))+
      geom_point_interactive(aes(tooltip=paste0("<b>Petal Length:</b> ",Petal.Length,"\n<b>Sepal Length: </b>",Sepal.Length,"\n<b>Species: </b>",Species)),size=2)+
  theme_bw()

tooltip_css <- "background-color:#e7eef3;font-family:Roboto;padding:10px;border-style:solid;border-width:2px;border-color:#125687;border-radius:5px;"

ggiraph(code=print(p),hover_css="cursor:pointer;stroke:black;fill-opacity:0.3",zoom_max=5,tooltip_extra_css=tooltip_css,tooltip_opacity=0.9)

Interactive scatterplot using ggiraph.

10.6 dygraphs

R package dygraphs provides R bindings for javascript library dygraphs for time series data.

library(dygraphs)

lungDeaths <- cbind(ldeaths, mdeaths, fdeaths)
dygraph(lungDeaths,main="Deaths from Lung Disease (UK)") %>%
  dyOptions(colors=c("#66C2A5","#FC8D62","#8DA0CB"))

Interactive time series plot using dygraph.

10.7 Network graph

R package networkD3 allows the use of interactive network graphs from the D3.js javascript library.

library(networkD3)

data(MisLinks,MisNodes)
forceNetwork(Links=MisLinks,Nodes=MisNodes,Source="source",
             Target="target",Value="value",NodeID="name",
             Group="group",opacity=0.4)

Interactive network plot.

10.8 leaflet

R package leaflet provides R bindings for javascript mapping library; leafletjs.

library(leaflet)

leaflet(height=500,width=700) %>%
  addTiles(urlTemplate='http://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png') %>%
  #addProviderTiles(providers$Esri.NatGeoWorldMap) %>%
  addMarkers(lat=57.639327,lng=18.288534,popup="RaukR") %>%
  setView(lat=57.639327,lng=18.288534,zoom=15)

Interactive map using leaflet.

10.9 crosstalk

R package crosstalk allows crosstalk enabled plotting libraries to be linked. Through the shared ‘key’ variable, data points can be manipulated simultaneously on two independent plots.

library(crosstalk)

shared_quakes <- SharedData$new(quakes[sample(nrow(quakes), 100),])
lf <- leaflet(shared_quakes,height=300) %>%
        addTiles(urlTemplate='http://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png') %>%
        addMarkers()
py <- plot_ly(shared_quakes,x=~depth,y=~mag,size=~stations,height=300) %>%
        add_markers()

htmltools::div(lf,py)

Linking independent plots using crosstalk.

11 ObservableJS

  • Quarto supports ObservableJS for interactive visualisations in the browser.

Pass data from R to OJS

irism <- iris
colnames(irism) <- gsub("[.]","_",tolower(colnames(irism)))
ojs_define(ojsd = irism)
ojsdata = transpose(ojsd)

Display as a table

viewof filtered_table = Inputs.table(ojsdata)

Define inputs

viewof x = Inputs.select(Object.keys(ojsdata[0]), {value: "sepal_length", multiple: false, label: "X axis"})
viewof y = Inputs.select(Object.keys(ojsdata[0]), {value: "sepal_width", multiple: false, label: "Y axis"})

Display plot

Plot.plot({
  marks: [
    Plot.dot(ojsdata, {
      x: x,
      y: y,
      fill: "species",
      title: (d) =>
        `${d.species} \n Petal length: ${d.petal_length} \n Sepal length: ${d.sepal_length}`
    })
  ],
  grid: true
})

ObservableJS in quarto documentation.

12 Diagrams

```{mermaid}
flowchart LR
  A[Hard edge] --> B(Round edge)
  B --> C{Decision}
  C --> D[Result one]
  C --> E[Result two]
```
flowchart LR
  A[Hard edge] --> B(Round edge)
  B --> C{Decision}
  C --> D[Result one]
  C --> E[Result two]

Diagram documentation.

13 Icons

To use fontawesome icons as shortcodes, quarto extension fontawesome needs to be installed.

Icons can be placed using shortcodes.

{{< fa lightbulb >}}
{{< fa exclamation >}}
{{< fa clipboard-list >}}
{{< fa comments >}}
{{< fa desktop >}}
{{< fa cloud >}}
{{< fa check >}}
{{< fa times >}}
{{< fa skull >}}
{{< fa skull size=2x >}}
{{< fa brands github >}}

Icons can be displayed using the HTML <i> tag. Note that not all icons may work.

Here is a <i class='fa fa-calendar'></i> calendar and a <i class='fa fa-couch'></i> couch.

Here is a calendar and a couch.

Icons can also be placed programatically through R using the R package fontawesome.

`r fontawesome::fa('lightbulb')`

Optional arguments are height and fill.

`r fontawesome::fa('lightbulb',height='30px',fill='steelblue')`

For full list of icons check out FontAwesome.

14 Call-Outs

Call-Out blocks are explained here.

::: {.callout-note}
This is a call-out.
:::

::: {.callout-warning}
This is a call-out.
:::

::: {.callout-important}
This is a call-out.
:::

::: {.callout-tip}
This is a call-out.
:::

::: {.callout-caution}
This is a call-out.
:::

::: {.callout-tip collapse="true"}
## Call-out with collapse

This content is hidden by default.
:::
Note

This is a call-out.

Warning

This is a call-out.

Important

This is a call-out.

Tip

This is a call-out.

Caution

This is a call-out.

This content is hidden by default.

15 Alerts

::: {.alert .alert-primary}
**Note:** This is an alert!
:::
::: {.alert .alert-secondary}
**Note:** This is an alert!
:::
::: {.alert .alert-success}
**Note:** This is a success alert!
:::
::: {.alert .alert-danger}
**Note:** This is a danger alert!
:::
::: {.alert .alert-warning}
**Note:** This is a warning alert!
:::
::: {.alert .alert-info}
**Note:** This is an info alert!
:::

Note: This is an alert!

Note: This is an alert!

Note: This is a success alert!

Note: This is a danger alert!

Note: This is a warning alert!

Note: This is an info alert!

16 General tips

  • Use level 2 heading as the highest level
  • Use quarto style chunk options
  • warnings and messages has been turned off in chunks globally
  • Declare all libraries at the beginning of the document
  • Add custom css under YAML if needed css: "my-theme.css"
  • Check out the Quarto website