quarto introduction

Author

Tony Duan

install quarto

install quarto CLI

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

install quarto pacakge

Code

install.packages("quarto")

check quarto version

in Terminal

Code

Terminal

quarto check

in R

Code

library(quarto)
quarto_version()

[1] '99.9.9'

quarto location

Code

quarto_path()

[1] "/usr/local/bin/quarto"

quarto code chunk

R

```{R}
version
```

Python

```{python}
import sys
print(sys.version)
```

Bash

```{bash}
echo "foo" 
```

calling variable between R and Python

There are R variable: r_var and Python version:python_var

```{r}
r_var=111
```

```{python}
python_var=222
```

calling python variable in R
calling R variable in Python

```{python}
r.r_var
```

111.0

```{r}
library(reticulate)
py$python_var
```

[1] 222

quarto code chunk option

in YAML header

---
title: "My Document"
execute:
  echo: false
jupyter: python3
---

eval： Evaluate the code chunk (if false, just echos the code into the output).
echo： Include the source code in output.
output： Include the results of executing the code in the output (true, false, or asis to indicate that the output is raw markdown and should not have any of Quarto’s standard enclosing markdown).
warning： Include warnings in the output.
error： Evaluate the code chunk (if false, just echos the code into the output).
include： Catch all for preventing any output (code or results) from being included (e.g. include: false suppresses all output from the code block).

in code chunk

Code

 #| eval: false

code chunk name

{r filename='code chunk name sample'}

Code

code chunk name sample

a=1
a

[1] 1

Rmarkdown

Code

*italics* and _italics_
**bold** and __bold__
superscript^2^
~~strikethrough~~
[link](www.rstudio.com)

Code

*italics*

italics

Code

**bold**

bold

Code

superscript^2^

superscript²

Code

~~strikethrough~~

~~strikethrough~~

Code

`highlight`

highlight

link

[link](www.rstudio.com)

link

tab

::: {.panel-tabset}

## Tab 1

This is tab 1


## Tab 2

This is tab 2

:::

Tab 1
Tab 2

This is tab 1

This is tab 2

column display

Code

::: columns
::: {.column width="40%"}
this column with 40% width
::: 

::: {.column width="60%"}
this column with 60% width
::: 

:::

this column with 40% width

this column with 60% width

Add a horizontal scroll bar

add hscroll.css file

Code

.hscroll {
  overflow: auto;
  white-space: nowrap;
}

add css option in YAML header

Code

---
css: hscroll.css
---

add # {.hscroll .scrollable} on the section which want to be Slide bar

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Maecenas dolor mauris, mattis non nunc nec, luctus aliquet magna. In tortor ante, aliquam eget felis eu, consectetur congue enim. Pellentesque pellentesque tincidunt lectus quis lacinia. Aliquam dolor sem, aliquet vitae aliquam eget, vehicula ac augue. Pellentesque molestie quam et commodo dignissim. Suspendisse potenti. Sed pellentesque metus non turpis condimentum molestie. Nullam accumsan urna nec luctus rutrum. Nunc dapibus auctor convallis. Praesent ac felis fermentum, venenatis elit vel, venenatis mi. Fusce non tellus risus. Phasellus elementum erat sit amet urna venenatis maximus. Nunc vehicula pretium scelerisque.

Add a vertical scroll bar

images1.png

images2.png

add a output hide bottom at quarto file

step 1. add foldableCodeBlcok.lua into blog root folder

Code

foldableCodeBlcok.lua

function CodeBlock(elem)
  if elem.classes and elem.classes:find("details") then
    local summary = "Code"
    if elem.attributes.summary then
      summary = elem.attributes.summary
    end
    return{
      pandoc.RawBlock(
        "html", "<details><summary>" .. summary .. "</summary>"
      ),
      elem,
      pandoc.RawBlock("html", "</details>")
    }
  end
end

step 2. add following line in `_quarto.yml`

Code

_quarto.yml

website:
  title: "quarto blog"

filters:
  - foldableCodeBlcok.lua

step 3. put following on code chunk:

{r, attr.output='.details summary="sessionInfo()"'}

Code

sessionInfo()

sessionInfo()

R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS 15.3.2

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Asia/Shanghai
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] reticulate_1.41.0 quarto_1.4.4     

loaded via a namespace (and not attached):
 [1] digest_0.6.37       later_1.4.1         fastmap_1.2.0      
 [4] Matrix_1.7-2        xfun_0.51           lattice_0.22-6     
 [7] knitr_1.49          htmltools_0.5.8.1   png_0.1-8          
[10] rmarkdown_2.29      ps_1.9.0            cli_3.6.4          
[13] processx_3.8.6.9000 grid_4.4.1          compiler_4.4.1     
[16] rstudioapi_0.17.1   tools_4.4.1         evaluate_1.0.3     
[19] Rcpp_1.0.14         yaml_2.3.10         rlang_1.1.5        
[22] jsonlite_2.0.0      htmlwidgets_1.6.4

render all quarto website

Code

Terminal

quarto render "tidymodel in R"

embed video

embed youtube

Code

<iframe width="640" height="480" src="https://www.youtube.com/embed/nku5zFMZAdU" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen>
</iframe>

embed bilibili

embed local video

Code

{{< video images/vv.mp4 height="600" >}}

embed audio

in code
in YAML header

Code

<figure>
<figcaption>click to play</figcaption>
<audio controls src="aa.mp3">
        Your browser does not support the
        <code>audio</code> element.
</audio>
</figure>

---
format:
  html:
    resources:
      - aa.mp3
---

Fonts

in _quarto.yml(for all page) or header(only for this page)

Code

_quarto.yml

format:
  html:
    mainfont:Times New Roman
    font-size: 120%;
  
# can find more font:https://developer.mozilla.org/en-US/docs/Web/CSS/font-family

source:https://quarto.org/docs/reference/formats/context.html

in page

Code

<p style="font-family: times, serif; font-size:500% ">This is font size 500%</p>

This is font size 500%

Code

<p style="font-family: times, serif; font-size:50% ">This is font size 50%</p>

This is font size 50%

Theme

in _quarto.yml(for all page) or header(only for this page)

Code

_quarto.yml

theme:
  light: cosmo
  dark: [cosmo, theme-dark.scss]

source:https://quarto.org/docs/output-formats/html-themes.html

Managing Execution

render a folder or file

Code

Terminal

quarto render introduction.qmd
quarto render subdir/

Freeze

You can use the freeze option to denote that computational documents should never be re-rendered during a global project render, or alternatively only be re-rendered when their source file changes:

in _quarto.yml(for all page) or header(only for this page)

Code

_quarto.yml

execute:
  freeze: true  # never re-render during project render

Code

_quarto.yml

execute:
  freeze: auto  # re-render only when source changes

Cache

You can use the cache option to cache the results of computations (using the knitr cache for R documents, and Jupyter Cache for Jupyter documents):

Code

_quarto.yml

execute:
  cache: true

Note that cache invalidation is triggered by changes in chunk source code (or other cache attributes you’ve defined). You may however need to manually refresh the cache if you know that some other input (or even time) has changed sufficiently to warrant an update. To do this, render either individual files or an entire project using the –cache-refresh option:

source:https://quarto.org/docs/projects/code-execution.html

Code

Terminal

quarto render mydoc.qmd --cache-refresh # single doc
quarto render --cache-refresh           # entire project

add comment

using giscus comment tool

https://giscus.app/

step 1 install giscus on github

https://github.com/apps/giscus

step 2 enable GitHub Discussions for your repository

step 3 add script to blog post

Code

'''
<script src="https://giscus.app/client.js"
        data-repo="[ENTER REPO HERE]"
        data-repo-id="[ENTER REPO ID HERE]"
        data-category="[ENTER CATEGORY NAME HERE]"
        data-category-id="[ENTER CATEGORY ID HERE]"
        data-mapping="pathname"
        data-strict="0"
        data-reactions-enabled="1"
        data-emit-metadata="0"
        data-input-position="bottom"
        data-theme="preferred_color_scheme"
        data-lang="en"
        crossorigin="anonymous"
        async>
</script>
'''

step 3b or using comment for all page

add into _quarto.yml

Code

_quarto.yml

format:
  html:
    include-after-body: 
         - text: <script src="https://giscus.app/client.js" data-repo="[ENTER REPO HERE]" data-repo-id="[ENTER REPO ID HERE]" data-category="[ENTER CATEGORY NAME HERE]" data-category-id="[ENTER CATEGORY ID HERE]" data-mapping="pathname" data-strict="0" data-reactions-enabled="1" data-emit-metadata="0" data-input-position="bottom" data-theme="preferred_color_scheme" data-lang="en" crossorigin="anonymous" async> </script>

quarto engine

Quarto is a multi-language, next generation version of R Markdown from RStudio, with many new features and capabilities

using R
using Python

by defalut,Quarto uses Knitr to execute R code

Code

title: "matplotlib demo"
format:
  html:
    code-fold: true

when set jupyter: python3 it will run quarto file with python

First, install jupyter & rpy2

Code

pip install jupyter
pip install rpy2

add engine jupyter: python3

Code

---
title: "ggplot2 demo"
author: "Norah Jones"
date: "5/22/2021"
format: 
  html:
    code-fold: true
jupyter: python3
---

Note that when rendering an .ipynb Quarto will not execute the cells within the notebook by default (the presumption being that you have already executed them while editing the notebook)

You can also specify this behavior within the notebook’s YAML front matter:

Code

---
title: "My Notebook"
execute: 
  enabled: true
---

Run R in python code chunk under python environment

Code

%load_ext rpy2.ipython

Code

%%R
print(R.version)

quarto output format

Code

---
title: "ggplot2 demo"
author: "Tony D"
date: "5/22/2021"
format: 
  html
---

Code

---
title: "ggplot2 demo"
author: "Tony D"
date: "5/22/2021"
format: 
  pdf
---

Code

---
title: "ggplot2 demo"
author: "Tony D"
date: "5/22/2021"
format: 
  docx
---

Code

---
title: "ggplot2 demo"
author: "Tony D"
date: "5/22/2021"
format: 
  pptx
---

Code

---
title: "ggplot2 demo"
author: "Tony D"
date: "5/22/2021"
format: 
  revealjs
---

Code

---
title: "ggplot2 demo"
author: "Tony D"
date: "5/22/2021"
format: 
  html: default
  revealjs: default
---

Reference

https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf

--- title: "quarto introduction" author: "Tony Duan" execute: warning: false error: false format: html: toc: true toc-location: right code-fold: show code-tools: true code-block-bg: true code-block-border-left: "#31BAE9" code-copy: true css: hscroll.css --- # install quarto ## install quarto CLI https://quarto.org/docs/get-started/ ## install quarto pacakge ```{r} #| eval: false install.packages("quarto") ``` # check quarto version ## in Terminal ```{bash filename="Terminal"} #| eval: false quarto check ``` ![](images/paste-1.png){width="600"} ## in R ```{r} library(quarto) quarto_version() ``` quarto location ```{r} quarto_path() ``` # quarto code chunk ## R ```{R} version ``` ## Python ```{python} import sys print(sys.version) ``` ## Bash ```{bash} echo "foo" ``` # calling variable between R and Python There are R variable: r_var and Python version:python_var ```{r} r_var=111 ``` ```{r} #| echo: false r_var=111 ``` ```{python} python_var=222 ``` ```{python} #| echo: false python_var=222 ``` ::: panel-tabset ## calling python variable in R ```{python} r.r_var ``` ```{python} #| echo: false r.r_var ``` ## calling R variable in Python ```{r} library(reticulate) py$python_var ``` ```{r} #| echo: false library(reticulate) py$python_var ``` ::: # quarto code chunk option ## in YAML header ``` yaml --- title: "My Document" execute: echo: false jupyter: python3 --- ``` - eval： Evaluate the code chunk (if false, just echos the code into the output). - echo： Include the source code in output. - output： Include the results of executing the code in the output (true, false, or asis to indicate that the output is raw markdown and should not have any of Quarto’s standard enclosing markdown). - warning： Include warnings in the output. - error： Evaluate the code chunk (if false, just echos the code into the output). - include： Catch all for preventing any output (code or results) from being included (e.g. include: false suppresses all output from the code block). ## in code chunk ```{bash} #| eval: false ``` # code chunk name `{r filename='code chunk name sample'}` ```{r filename='code chunk name sample'} a=1 a ``` # Rmarkdown ```{r} #| eval: false *italics* and _italics_ **bold** and __bold__ superscript^2^ ~~strikethrough~~ [link](www.rstudio.com) ``` ```{r} #| eval: false *italics* ``` *italics* ```{r} #| eval: false **bold** ``` **bold** ```{r} #| eval: false superscript^2^ ``` superscript^2^ ```{r} #| eval: false ~~strikethrough~~ ``` ~~strikethrough~~ ```{r} #| eval: false `highlight` ``` `highlight` ## link ```` [link](www.rstudio.com) ```` [link](www.rstudio.com) ## tab ```` ::: {.panel-tabset} ## Tab 1 This is tab 1 ## Tab 2 This is tab 2 ::: ```` ::: panel-tabset ### Tab 1 This is tab 1 ### Tab 2 This is tab 2 ::: ## column display ```{r} #| eval: false ::: columns ::: {.column width="40%"} this column with 40% width ::: ::: {.column width="60%"} this column with 60% width ::: ::: ``` ::::: columns ::: {.column width="40%"} this column with 40% width ::: ::: {.column width="60%"} this column with 60% width ::: ::::: # Add a horizontal scroll bar - add hscroll.css file ```{r} #| eval: false .hscroll { overflow: auto; white-space: nowrap; } ``` - add css option in YAML header ```{r} #| eval: false --- css: hscroll.css --- ``` - add `# {.hscroll .scrollable}` on the section which want to be Slide bar # {.hscroll .scrollable} Lorem ipsum dolor sit amet, consectetur adipiscing elit. Maecenas dolor mauris, mattis non nunc nec, luctus aliquet magna. In tortor ante, aliquam eget felis eu, consectetur congue enim. Pellentesque pellentesque tincidunt lectus quis lacinia. Aliquam dolor sem, aliquet vitae aliquam eget, vehicula ac augue. Pellentesque molestie quam et commodo dignissim. Suspendisse potenti. Sed pellentesque metus non turpis condimentum molestie. Nullam accumsan urna nec luctus rutrum. Nunc dapibus auctor convallis. Praesent ac felis fermentum, venenatis elit vel, venenatis mi. Fusce non tellus risus. Phasellus elementum erat sit amet urna venenatis maximus. Nunc vehicula pretium scelerisque. # Add a vertical scroll bar ::: {.scroll-container style="overflow-x: scroll; height: 600px;"} images1.png images2.png ::: ::: {.scroll-container style="overflow-x: scroll; height: 600px;"} ![](images/12.png){width="900"} ![](images/13.png){width="900"} ::: # add a output hide bottom at quarto file ## step 1. add foldableCodeBlcok.lua into blog root folder ```{r filename='foldableCodeBlcok.lua'} #| eval: false function CodeBlock(elem) if elem.classes and elem.classes:find("details") then local summary = "Code" if elem.attributes.summary then summary = elem.attributes.summary end return{ pandoc.RawBlock( "html", "<details><summary>" .. summary .. "</summary>" ), elem, pandoc.RawBlock("html", "</details>") } end end ``` ## step 2. add following line in `_quarto.yml` ```{r filename='_quarto.yml'} #| eval: false website: title: "quarto blog" filters: - foldableCodeBlcok.lua ``` ## step 3. put following on code chunk: `{r, attr.output='.details summary="sessionInfo()"'}` ```{r, attr.output='.details summary="sessionInfo()"'} #| eval: true sessionInfo() ``` # render all quarto website ```{r filename="Terminal"} #| eval: false quarto render "tidymodel in R" ``` # embed video ## embed youtube ```{r} #| eval: false <iframe width="640" height="480" src="https://www.youtube.com/embed/nku5zFMZAdU" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen> </iframe> ``` ## embed bilibili <iframe width="640" height="480" src="//player.bilibili.com/player.html?isOutside=true&aid=892286280&bvid=BV1pP4y1G7hU&cid=461709819&p=1&autoplay=0&muted=false&danmaku=0" scrolling="no" border="0" frameborder="no" framespacing="0" allowfullscreen="true" sandbox="allow-top-navigation allow-same-origin allow-forms allow-scripts"></iframe> ## embed local video ```{r} #| eval: false {{< video images/vv.mp4 height="600" >}} ``` # embed audio ::: panel-tabset ## in code ```{r} #| eval: false <figure> <figcaption>click to play</figcaption> <audio controls src="aa.mp3"> Your browser does not support the <code>audio</code> element. </audio> </figure> ``` ## in YAML header ``` yaml --- format: html: resources: - aa.mp3 --- ``` ::: # Fonts ## in _quarto.yml(for all page) or header(only for this page) ```{r filename="_quarto.yml"} #| eval: false format: html: mainfont:Times New Roman font-size: 120%; # can find more font:https://developer.mozilla.org/en-US/docs/Web/CSS/font-family ``` source:https://quarto.org/docs/reference/formats/context.html ## in page ```{r} #| eval: false <p style="font-family: times, serif; font-size:500% ">This is font size 500%</p> ``` <p style="font-family: times, serif; font-size:500% ">This is font size 500%</p> ```{r} #| eval: false <p style="font-family: times, serif; font-size:50% ">This is font size 50%</p> ``` <p style="font-family: times, serif; font-size:50% ">This is font size 50%</p> # Theme in _quarto.yml(for all page) or header(only for this page) ```{r filename="_quarto.yml"} #| eval: false theme: light: cosmo dark: [cosmo, theme-dark.scss] ``` source:https://quarto.org/docs/output-formats/html-themes.html # Managing Execution ## render a folder or file ```{bash filename="Terminal"} #| eval: false quarto render introduction.qmd quarto render subdir/ ``` ## Freeze You can use the freeze option to denote that computational documents should never be re-rendered during a global project render, or alternatively only be re-rendered when their source file changes: in _quarto.yml(for all page) or header(only for this page) ```{r filename="_quarto.yml"} #| eval: false execute: freeze: true # never re-render during project render ``` ```{r filename="_quarto.yml"} #| eval: false execute: freeze: auto # re-render only when source changes ``` ## Cache You can use the cache option to cache the results of computations (using the knitr cache for R documents, and Jupyter Cache for Jupyter documents): ```{r filename="_quarto.yml"} #| eval: false execute: cache: true ``` Note that cache invalidation is triggered by changes in chunk source code (or other cache attributes you’ve defined). You may however need to manually refresh the cache if you know that some other input (or even time) has changed sufficiently to warrant an update. To do this, render either individual files or an entire project using the --cache-refresh option: source:https://quarto.org/docs/projects/code-execution.html ```{r filename="Terminal"} #| eval: false quarto render mydoc.qmd --cache-refresh # single doc quarto render --cache-refresh # entire project ``` # add comment ## using giscus comment tool https://giscus.app/ ### step 1 install giscus on github https://github.com/apps/giscus ### step 2 enable GitHub Discussions for your repository ![](images/clipboard-2990658216.png) ### step 3 add script to blog post ```{r} #| eval: false ''' <script src="https://giscus.app/client.js" data-repo="[ENTER REPO HERE]" data-repo-id="[ENTER REPO ID HERE]" data-category="[ENTER CATEGORY NAME HERE]" data-category-id="[ENTER CATEGORY ID HERE]" data-mapping="pathname" data-strict="0" data-reactions-enabled="1" data-emit-metadata="0" data-input-position="bottom" data-theme="preferred_color_scheme" data-lang="en" crossorigin="anonymous" async> </script> ''' ``` #### step 3b or using comment for all page add into _quarto.yml ```{r filename="_quarto.yml"} #| eval: false format: html: include-after-body: - text: <script src="https://giscus.app/client.js" data-repo="[ENTER REPO HERE]" data-repo-id="[ENTER REPO ID HERE]" data-category="[ENTER CATEGORY NAME HERE]" data-category-id="[ENTER CATEGORY ID HERE]" data-mapping="pathname" data-strict="0" data-reactions-enabled="1" data-emit-metadata="0" data-input-position="bottom" data-theme="preferred_color_scheme" data-lang="en" crossorigin="anonymous" async> </script> ``` # quarto engine Quarto is a multi-language, next generation version of R Markdown from RStudio, with many new features and capabilities ::: panel-tabset ## using R by defalut,Quarto uses Knitr to execute R code ```{r} #| eval: false #| title: "matplotlib demo" format: html: code-fold: true ``` ## using Python when set jupyter: python3 it will run quarto file with python ### First, install jupyter & rpy2 ```{bash} #| eval: false pip install jupyter pip install rpy2 ``` ### add engine jupyter: python3 ```{r} #| eval: false --- title: "ggplot2 demo" author: "Norah Jones" date: "5/22/2021" format: html: code-fold: true jupyter: python3 --- ``` Note that when rendering an .ipynb Quarto will not execute the cells within the notebook by default (the presumption being that you have already executed them while editing the notebook) You can also specify this behavior within the notebook’s YAML front matter: ```{r} #| eval: false --- title: "My Notebook" execute: enabled: true --- ``` ### Run R in python code chunk under python environment ```{python} #| eval: false %load_ext rpy2.ipython ``` ```{python} #| eval: false %%R print(R.version) ``` ::: # quarto output format ::: panel-tabset ## html ```{r} #| eval: false --- title: "ggplot2 demo" author: "Tony D" date: "5/22/2021" format: html --- ``` ## pdf ```{r} #| eval: false --- title: "ggplot2 demo" author: "Tony D" date: "5/22/2021" format: pdf --- ``` ## MS words ```{r} #| eval: false --- title: "ggplot2 demo" author: "Tony D" date: "5/22/2021" format: docx --- ``` ## MS PowerPoint ```{r} #| eval: false --- title: "ggplot2 demo" author: "Tony D" date: "5/22/2021" format: pptx --- ``` ## Revealjs ```{r} #| eval: false --- title: "ggplot2 demo" author: "Tony D" date: "5/22/2021" format: revealjs --- ``` ## multi ouput format at once ```{r} #| eval: false --- title: "ggplot2 demo" author: "Tony D" date: "5/22/2021" format: html: default revealjs: default --- ``` ## Others <iframe width="900" height="600" src="https://quarto.org/docs/output-formats/all-formats.html"></iframe> ::: # Reference https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf

install quarto

install quarto CLI

install quarto pacakge

check quarto version

in Terminal

in R

quarto code chunk

R

Python

Bash

calling variable between R and Python

quarto code chunk option

in YAML header

in code chunk

code chunk name

Rmarkdown

link

tab

column display

Add a horizontal scroll bar

Add a vertical scroll bar

add a output hide bottom at quarto file

step 1. add foldableCodeBlcok.lua into blog root folder

step 2. add following line in _quarto.yml

step 3. put following on code chunk:

render all quarto website

embed video

embed youtube

embed bilibili

embed local video

embed audio

Fonts

in _quarto.yml(for all page) or header(only for this page)

in page

Theme

Managing Execution

render a folder or file

Freeze

Cache

add comment

using giscus comment tool

step 1 install giscus on github

step 2 enable GitHub Discussions for your repository

step 3 add script to blog post

step 3b or using comment for all page

quarto engine

First, install jupyter & rpy2

add engine jupyter: python3

Run R in python code chunk under python environment

quarto output format

Reference

step 2. add following line in `_quarto.yml`