Documents

pyOpenSci Fall Festival 2024: Reproducible reports and presentations
with Quarto and Great Tables

Mine Çetinkaya Rundel with adaptations by Tracy Teal

Anatomy of a Quarto document

Components

Metadata: YAML
Text: Markdown
Code: Executed via jupyter (or knitr)

Weave it all together, and you have beautiful, powerful, and useful outputs!

Literate programming

Literate programming is writing out the program logic in a human language with included (separated by a primitive markup) code snippets and macros.

---
title: plotnine demo
date: 11/01/2024
format: html
---

There is a relationship between flipper length and body mass.

```{python}
#| label: fig-penguins
import plotnine as p9
from palmerpenguins import load_penguins

penguins = load_penguins()

(
    p9.ggplot(
        penguins, 
        p9.aes(x = "flipper_length_mm", y = "body_mass_g")
    )
    + p9.geom_point()
    + p9.stat_smooth(method="lm")
    + p9.labs(
        x = "Flipper length (mm)", 
        y = "Body mass (g)", 
        title = "Body mass vs. flipper length of Palmer Penguins"
    )
)
```

Metadata

YAML

“Yet Another Markup Language” or “YAML Ain’t Markup Language” is used to provide document level metadata.

---
key: value
---

Output options

---
format: something
---

---
format: html
---

---
format: pdf
---

---
format: revealjs
---

Output option arguments

Indentation matters!

---
format: 
  html:
    toc: true
    code-fold: true
---

YAML validation

Invalid: No space after :

---
format:html
---

Invalid: Read as missing

---
format:
html
---

Valid, but needs next object

---
format: 
  html:
---

YAML validation

There are multiple ways of formatting valid YAML:

Valid: There’s a space after :

format: html

Valid: There are 2 spaces a new line and no trailing :

format:
  html

Valid: format: html with selections made with proper indentation

format: 
  html:
    toc: true

Why YAML?

To avoid manually typing out all the options, every time when rendering via the CLI:

Define format

quarto render document.qmd --to html

Define format and format options

quarto render document.qmd --to html -M code-fold:true

Define format, format options, and values for parameters

quarto render document.qmd --to html -M code-fold:true -P alpha:0.2 -P ratio:0.3

Quarto linting

Lint, or a linter, is a static code analysis tool used to flag programming errors, bugs, stylistic errors and suspicious constructs.

Quarto YAML Intelligence

VS Code provides rich tab-completion - start a word and tab to complete, or Ctrl + space to see all available options.

Your turn

Open hello-penguins.qmd in VS Code.
Try Ctrl + space to see the available YAML options.
Try out the tab-completion of any options you remember or use the HTML reference (https://quarto.org/docs/reference/formats/html.html) as needed.

03:00

List of valid YAML fields

Many YAML fields are common across various outputs
But also each output type has its own set of valid YAML fields and options
Definitive list: quarto.org/docs/reference/formats/html

Text

TL;DR

Pretty much everything you know about markdown formatting works with Quarto

Text Formatting

Markdown syntax:	Output:
`italics and bold`	italics and bold
`superscript^2^ / subscript~2~`	superscript² / subscript₂
`~~strikethrough~~`	~~strikethrough~~
`verbatim code`	`verbatim code`

Headings

Markdown syntax:	Output:
`# Header 1`	Header 1
`## Header 2`	Header 2
`### Header 3`	Header 3
`#### Header 4`	Header 4
`##### Header 5`	Header 5
`###### Header 6`	Header 6

Links

Several types of links / hyperlinks:

Markdown syntax:

You can embed [named hyperlinks](https://quarto.org/),
direct urls like <https://quarto.org/>, and links to 
[other places](#quarto-anatomy) in 
the document. 

The syntax is similar for embedding an
inline image: 

![Penguins playing with ball](images/penguins-quarto-ball.png).

Output:

You can embed named hyperlinks, direct urls like https://quarto.org/, and links to other places in the document.

The syntax is similar for embedding an inline image:

Penguins playing with ball .

Lists

Unordered lists:

Markdown syntax:

-   unordered list         
    -   sub-item 1         
    -   sub-item 1         
        -   sub-sub-item 1

Output:

unordered list
- sub-item 1
- sub-item 1
  - sub-sub-item 1

Ordered lists:

Markdown syntax:

1. ordered list            
2. item 2                  
    i. sub-item 1          
         A.  sub-sub-item 1

Output:

ordered list
item 2
1. sub-item 1
  1. sub-sub-item 1

Quotes

Markdown syntax:

> 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 human beings what we want a computer to do. 
>
> Donald Knuth, Literate Programming

Output:

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 human beings what we want a computer to do.

Donald Knuth, Literate Programming

Divs

Pandoc, and therefore Quarto, can parse fenced div blocks:

You can think of a ::: div as a HTML <div> but it can also apply in specific situations to content in PDF or other formats:

Markdown syntax:

::: {style="border-left:10px solid red;padding-left:5px"}
This content is styled with a thick red border and some padding next to it.
:::

Output:

This content is styled with a thick red border and some padding next to it.

Divs with pre-defined classes

These can often apply between formats:

::: {.unnumbered .unlisted}
Text
:::

Spans

[text]{.class} spans can be thought of a <span .class>Text</span>, but again are a bit more transferable if using Pandoc/Quarto native attributes.

Markdown syntax:

This is text is colored [red]{style="color:red;"}.

Output:

This is text is colored red.

Your turn

Open markdown-syntax.qmd in VS Code.
Follow the instructions in the document, then exchange one new thing you’ve learned with your neighbor.

05:00

Callouts

Markdown syntax:

::: callout-note
Note that there are five types of callouts, including: 
`note`, `tip`, `warning`, `caution`, and `important`.
:::

Output:

Note

Note that there are five types of callouts, including: note, tip, warning, caution, and important.

More callouts

Warning

Callouts provide a simple way to attract attention, for example, to this warning.

Important

This is important! Callouts will really improve your writing.

Caution

Here is something under construction.

Caption

Tip with caption.

Your turn

Open callout-boxes.qmd and render the document.
Using the visual editor, change the type of the first callouts box and then re-render. Also play with the options to change its appearance.
Add a caption to the second callout box.
Make the third callout box collapsible. Then, switch over to the source editor to inspect the markdown code.
Change the format to PDF and re-render.

03:00

Footnotes

Pandoc supports numbering and formatting footnotes.
In Quarto, the footnote is placed at the bottom of the slide in presentations, whereas in a document it’s hoverable or at the end of the document.

Inline footnotes

Markdown syntax:

Here is an inline note.^[Inlines notes are easier to write,
since you don't have to pick an identifier and move down to
type the note.]

Output:

Here is an inline note.¹

Numbered footnotes

Markdown syntax:

Here is an footnore reference[^1]

[^1]: This can be easy in some situations when you have a really long note or
don't want to inline complex outputs.

Output: Here is an footnore reference¹

Code

Anatomy of a code chunk

```{python}
#| label: penguins

!pip install palmerpenguins
!pip install plotnine
!pip install pandas

import pandas as pd
from palmerpenguins import load_penguins

penguins = load_penguins()

penguins["species"].unique()
```

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[notice] A new release of pip is available: 24.2 -> 24.3.1
[notice] To update, run: pip install --upgrade pip
Collecting plotnine
  Using cached plotnine-0.14.0-py3-none-any.whl.metadata (9.3 kB)
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  Using cached mizani-0.13.0-py3-none-any.whl.metadata (4.7 kB)
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Using cached plotnine-0.14.0-py3-none-any.whl (1.3 MB)
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Installing collected packages: mizani, plotnine
Successfully installed mizani-0.13.0 plotnine-0.14.0

[notice] A new release of pip is available: 24.2 -> 24.3.1
[notice] To update, run: pip install --upgrade pip
Requirement already satisfied: pandas in /usr/local/Caskroom/mambaforge/base/lib/python3.10/site-packages (2.2.2)
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[notice] A new release of pip is available: 24.2 -> 24.3.1
[notice] To update, run: pip install --upgrade pip

array(['Adelie', 'Gentoo', 'Chinstrap'], dtype=object)

Has 3x backticks on each end
Engine (python) is indicated between curly braces {python}
Options stated with the #| (hashpipe): #| option1: value

Code, who is it for?

The way you display code is very different for different contexts.
In a teaching scenario like today, I really want to display code.
In a business, you may want to have a data-science facing output which displays the source code AND a stakeholder-facing output which hides the code.

Code

If you simply want code formatting but don’t want to execute the code:

Option 1: Use 3x back ticks + the language ```python

```python
penguins.head()
```

Option 2: Add eval: false as chunk option

```{python}
#| eval: false
penguins.head()
```

Showing and hiding code with `echo`

The echo option shows the code when set to true and hides it when set to false.
If you want to both execute the code and return the full code including backticks (like in a teaching scenario) echo: fenced is your friend!

```{python}
1 + 1
```

Tables and figures

In reproducible reports and manuscripts, the most commonly included code outputs are tables and figures.
So they get their own special sections in our deep dive!

Tables

Markdown tables

Markdown syntax:

| Right | Left | Default | Center |
|------:|:-----|---------|:------:|
|   12  |  12  |    12   |    12  |
|  123  |  123 |   123   |   123  |
|    1  |    1 |     1   |     1  |

Output:

Right	Left	Default	Center
12	12	12	12
123	123	123	123
1	1	1	1

Grid tables

Markdown syntax:

+---------------+---------------+--------------------+
| Fruit         | Price         | Advantages         |
+===============+===============+====================+
| Bananas       | $1.34         | - built-in wrapper |
|               |               | - bright color     |
+---------------+---------------+--------------------+
| Oranges       | $2.10         | - cures scurvy     |
|               |               | - tasty            |
+---------------+---------------+--------------------+

: Sample grid table.

Output:

Sample grid table.
Fruit	Price	Advantages
Bananas	$1.34	built-in wrapper bright color
Oranges	$2.10	cures scurvy tasty

Grid tables: Alignment

Alignments can be specified as with pipe tables, by putting colons at the boundaries of the separator line after the header:

+---------------+---------------+--------------------+
| Right         | Left          | Centered           |
+==============:+:==============+:==================:+
| Bananas       | $1.34         | built-in wrapper   |
+---------------+---------------+--------------------+

For headerless tables, the colons go on the top line instead:

+--------------:+:--------------+:------------------:+
| Right         | Left          | Centered           |
+---------------+---------------+--------------------+

Grid tables: Authoring

Note that grid tables are quite awkward to write with a plain text editor because unlike pipe tables, the column indicators must align.
The Visual Editor can assist in making these tables!

Tables from code

If you are using pandas to work with your data, you can convert a pandas DataFrame to an HTML table using the DataFrame.to_html() method:

penguins.to_html(index=False)

species	island	bill_length_mm	bill_depth_mm	flipper_length_mm	body_mass_g	sex	year
Adelie	Torgersen	39.1	18.7	181.0	3750.0	male	2007
Adelie	Torgersen	39.5	17.4	186.0	3800.0	female	2007
Adelie	Torgersen	40.3	18.0	195.0	3250.0	female	2007
Adelie	Torgersen	NaN	NaN	NaN	NaN	NaN	2007
Adelie	Torgersen	36.7	19.3	193.0	3450.0	female	2007
Adelie	Torgersen	39.3	20.6	190.0	3650.0	male	2007
Adelie	Torgersen	38.9	17.8	181.0	3625.0	female	2007
Adelie	Torgersen	39.2	19.6	195.0	4675.0	male	2007
Adelie	Torgersen	34.1	18.1	193.0	3475.0	NaN	2007
Adelie	Torgersen	42.0	20.2	190.0	4250.0	NaN	2007
Adelie	Torgersen	37.8	17.1	186.0	3300.0	NaN	2007
Adelie	Torgersen	37.8	17.3	180.0	3700.0	NaN	2007
Adelie	Torgersen	41.1	17.6	182.0	3200.0	female	2007
Adelie	Torgersen	38.6	21.2	191.0	3800.0	male	2007
Adelie	Torgersen	34.6	21.1	198.0	4400.0	male	2007
Adelie	Torgersen	36.6	17.8	185.0	3700.0	female	2007
Adelie	Torgersen	38.7	19.0	195.0	3450.0	female	2007
Adelie	Torgersen	42.5	20.7	197.0	4500.0	male	2007
Adelie	Torgersen	34.4	18.4	184.0	3325.0	female	2007
Adelie	Torgersen	46.0	21.5	194.0	4200.0	male	2007
Adelie	Biscoe	37.8	18.3	174.0	3400.0	female	2007
Adelie	Biscoe	37.7	18.7	180.0	3600.0	male	2007
Adelie	Biscoe	35.9	19.2	189.0	3800.0	female	2007
Adelie	Biscoe	38.2	18.1	185.0	3950.0	male	2007
Adelie	Biscoe	38.8	17.2	180.0	3800.0	male	2007
Adelie	Biscoe	35.3	18.9	187.0	3800.0	female	2007
Adelie	Biscoe	40.6	18.6	183.0	3550.0	male	2007
Adelie	Biscoe	40.5	17.9	187.0	3200.0	female	2007
Adelie	Biscoe	37.9	18.6	172.0	3150.0	female	2007
Adelie	Biscoe	40.5	18.9	180.0	3950.0	male	2007
Adelie	Dream	39.5	16.7	178.0	3250.0	female	2007
Adelie	Dream	37.2	18.1	178.0	3900.0	male	2007
Adelie	Dream	39.5	17.8	188.0	3300.0	female	2007
Adelie	Dream	40.9	18.9	184.0	3900.0	male	2007
Adelie	Dream	36.4	17.0	195.0	3325.0	female	2007
Adelie	Dream	39.2	21.1	196.0	4150.0	male	2007
Adelie	Dream	38.8	20.0	190.0	3950.0	male	2007
Adelie	Dream	42.2	18.5	180.0	3550.0	female	2007
Adelie	Dream	37.6	19.3	181.0	3300.0	female	2007
Adelie	Dream	39.8	19.1	184.0	4650.0	male	2007
Adelie	Dream	36.5	18.0	182.0	3150.0	female	2007
Adelie	Dream	40.8	18.4	195.0	3900.0	male	2007
Adelie	Dream	36.0	18.5	186.0	3100.0	female	2007
Adelie	Dream	44.1	19.7	196.0	4400.0	male	2007
Adelie	Dream	37.0	16.9	185.0	3000.0	female	2007
Adelie	Dream	39.6	18.8	190.0	4600.0	male	2007
Adelie	Dream	41.1	19.0	182.0	3425.0	male	2007
Adelie	Dream	37.5	18.9	179.0	2975.0	NaN	2007
Adelie	Dream	36.0	17.9	190.0	3450.0	female	2007
Adelie	Dream	42.3	21.2	191.0	4150.0	male	2007
Adelie	Biscoe	39.6	17.7	186.0	3500.0	female	2008
Adelie	Biscoe	40.1	18.9	188.0	4300.0	male	2008
Adelie	Biscoe	35.0	17.9	190.0	3450.0	female	2008
Adelie	Biscoe	42.0	19.5	200.0	4050.0	male	2008
Adelie	Biscoe	34.5	18.1	187.0	2900.0	female	2008
Adelie	Biscoe	41.4	18.6	191.0	3700.0	male	2008
Adelie	Biscoe	39.0	17.5	186.0	3550.0	female	2008
Adelie	Biscoe	40.6	18.8	193.0	3800.0	male	2008
Adelie	Biscoe	36.5	16.6	181.0	2850.0	female	2008
Adelie	Biscoe	37.6	19.1	194.0	3750.0	male	2008
Adelie	Biscoe	35.7	16.9	185.0	3150.0	female	2008
Adelie	Biscoe	41.3	21.1	195.0	4400.0	male	2008
Adelie	Biscoe	37.6	17.0	185.0	3600.0	female	2008
Adelie	Biscoe	41.1	18.2	192.0	4050.0	male	2008
Adelie	Biscoe	36.4	17.1	184.0	2850.0	female	2008
Adelie	Biscoe	41.6	18.0	192.0	3950.0	male	2008
Adelie	Biscoe	35.5	16.2	195.0	3350.0	female	2008
Adelie	Biscoe	41.1	19.1	188.0	4100.0	male	2008
Adelie	Torgersen	35.9	16.6	190.0	3050.0	female	2008
Adelie	Torgersen	41.8	19.4	198.0	4450.0	male	2008
Adelie	Torgersen	33.5	19.0	190.0	3600.0	female	2008
Adelie	Torgersen	39.7	18.4	190.0	3900.0	male	2008
Adelie	Torgersen	39.6	17.2	196.0	3550.0	female	2008
Adelie	Torgersen	45.8	18.9	197.0	4150.0	male	2008
Adelie	Torgersen	35.5	17.5	190.0	3700.0	female	2008
Adelie	Torgersen	42.8	18.5	195.0	4250.0	male	2008
Adelie	Torgersen	40.9	16.8	191.0	3700.0	female	2008
Adelie	Torgersen	37.2	19.4	184.0	3900.0	male	2008
Adelie	Torgersen	36.2	16.1	187.0	3550.0	female	2008
Adelie	Torgersen	42.1	19.1	195.0	4000.0	male	2008
Adelie	Torgersen	34.6	17.2	189.0	3200.0	female	2008
Adelie	Torgersen	42.9	17.6	196.0	4700.0	male	2008
Adelie	Torgersen	36.7	18.8	187.0	3800.0	female	2008
Adelie	Torgersen	35.1	19.4	193.0	4200.0	male	2008
Adelie	Dream	37.3	17.8	191.0	3350.0	female	2008
Adelie	Dream	41.3	20.3	194.0	3550.0	male	2008
Adelie	Dream	36.3	19.5	190.0	3800.0	male	2008
Adelie	Dream	36.9	18.6	189.0	3500.0	female	2008
Adelie	Dream	38.3	19.2	189.0	3950.0	male	2008
Adelie	Dream	38.9	18.8	190.0	3600.0	female	2008
Adelie	Dream	35.7	18.0	202.0	3550.0	female	2008
Adelie	Dream	41.1	18.1	205.0	4300.0	male	2008
Adelie	Dream	34.0	17.1	185.0	3400.0	female	2008
Adelie	Dream	39.6	18.1	186.0	4450.0	male	2008
Adelie	Dream	36.2	17.3	187.0	3300.0	female	2008
Adelie	Dream	40.8	18.9	208.0	4300.0	male	2008
Adelie	Dream	38.1	18.6	190.0	3700.0	female	2008
Adelie	Dream	40.3	18.5	196.0	4350.0	male	2008
Adelie	Dream	33.1	16.1	178.0	2900.0	female	2008
Adelie	Dream	43.2	18.5	192.0	4100.0	male	2008
Adelie	Biscoe	35.0	17.9	192.0	3725.0	female	2009
Adelie	Biscoe	41.0	20.0	203.0	4725.0	male	2009
Adelie	Biscoe	37.7	16.0	183.0	3075.0	female	2009
Adelie	Biscoe	37.8	20.0	190.0	4250.0	male	2009
Adelie	Biscoe	37.9	18.6	193.0	2925.0	female	2009
Adelie	Biscoe	39.7	18.9	184.0	3550.0	male	2009
Adelie	Biscoe	38.6	17.2	199.0	3750.0	female	2009
Adelie	Biscoe	38.2	20.0	190.0	3900.0	male	2009
Adelie	Biscoe	38.1	17.0	181.0	3175.0	female	2009
Adelie	Biscoe	43.2	19.0	197.0	4775.0	male	2009
Adelie	Biscoe	38.1	16.5	198.0	3825.0	female	2009
Adelie	Biscoe	45.6	20.3	191.0	4600.0	male	2009
Adelie	Biscoe	39.7	17.7	193.0	3200.0	female	2009
Adelie	Biscoe	42.2	19.5	197.0	4275.0	male	2009
Adelie	Biscoe	39.6	20.7	191.0	3900.0	female	2009
Adelie	Biscoe	42.7	18.3	196.0	4075.0	male	2009
Adelie	Torgersen	38.6	17.0	188.0	2900.0	female	2009
Adelie	Torgersen	37.3	20.5	199.0	3775.0	male	2009
Adelie	Torgersen	35.7	17.0	189.0	3350.0	female	2009
Adelie	Torgersen	41.1	18.6	189.0	3325.0	male	2009
Adelie	Torgersen	36.2	17.2	187.0	3150.0	female	2009
Adelie	Torgersen	37.7	19.8	198.0	3500.0	male	2009
Adelie	Torgersen	40.2	17.0	176.0	3450.0	female	2009
Adelie	Torgersen	41.4	18.5	202.0	3875.0	male	2009
Adelie	Torgersen	35.2	15.9	186.0	3050.0	female	2009
Adelie	Torgersen	40.6	19.0	199.0	4000.0	male	2009
Adelie	Torgersen	38.8	17.6	191.0	3275.0	female	2009
Adelie	Torgersen	41.5	18.3	195.0	4300.0	male	2009
Adelie	Torgersen	39.0	17.1	191.0	3050.0	female	2009
Adelie	Torgersen	44.1	18.0	210.0	4000.0	male	2009
Adelie	Torgersen	38.5	17.9	190.0	3325.0	female	2009
Adelie	Torgersen	43.1	19.2	197.0	3500.0	male	2009
Adelie	Dream	36.8	18.5	193.0	3500.0	female	2009
Adelie	Dream	37.5	18.5	199.0	4475.0	male	2009
Adelie	Dream	38.1	17.6	187.0	3425.0	female	2009
Adelie	Dream	41.1	17.5	190.0	3900.0	male	2009
Adelie	Dream	35.6	17.5	191.0	3175.0	female	2009
Adelie	Dream	40.2	20.1	200.0	3975.0	male	2009
Adelie	Dream	37.0	16.5	185.0	3400.0	female	2009
Adelie	Dream	39.7	17.9	193.0	4250.0	male	2009
Adelie	Dream	40.2	17.1	193.0	3400.0	female	2009
Adelie	Dream	40.6	17.2	187.0	3475.0	male	2009
Adelie	Dream	32.1	15.5	188.0	3050.0	female	2009
Adelie	Dream	40.7	17.0	190.0	3725.0	male	2009
Adelie	Dream	37.3	16.8	192.0	3000.0	female	2009
Adelie	Dream	39.0	18.7	185.0	3650.0	male	2009
Adelie	Dream	39.2	18.6	190.0	4250.0	male	2009
Adelie	Dream	36.6	18.4	184.0	3475.0	female	2009
Adelie	Dream	36.0	17.8	195.0	3450.0	female	2009
Adelie	Dream	37.8	18.1	193.0	3750.0	male	2009
Adelie	Dream	36.0	17.1	187.0	3700.0	female	2009
Adelie	Dream	41.5	18.5	201.0	4000.0	male	2009
Gentoo	Biscoe	46.1	13.2	211.0	4500.0	female	2007
Gentoo	Biscoe	50.0	16.3	230.0	5700.0	male	2007
Gentoo	Biscoe	48.7	14.1	210.0	4450.0	female	2007
Gentoo	Biscoe	50.0	15.2	218.0	5700.0	male	2007
Gentoo	Biscoe	47.6	14.5	215.0	5400.0	male	2007
Gentoo	Biscoe	46.5	13.5	210.0	4550.0	female	2007
Gentoo	Biscoe	45.4	14.6	211.0	4800.0	female	2007
Gentoo	Biscoe	46.7	15.3	219.0	5200.0	male	2007
Gentoo	Biscoe	43.3	13.4	209.0	4400.0	female	2007
Gentoo	Biscoe	46.8	15.4	215.0	5150.0	male	2007
Gentoo	Biscoe	40.9	13.7	214.0	4650.0	female	2007
Gentoo	Biscoe	49.0	16.1	216.0	5550.0	male	2007
Gentoo	Biscoe	45.5	13.7	214.0	4650.0	female	2007
Gentoo	Biscoe	48.4	14.6	213.0	5850.0	male	2007
Gentoo	Biscoe	45.8	14.6	210.0	4200.0	female	2007
Gentoo	Biscoe	49.3	15.7	217.0	5850.0	male	2007
Gentoo	Biscoe	42.0	13.5	210.0	4150.0	female	2007
Gentoo	Biscoe	49.2	15.2	221.0	6300.0	male	2007
Gentoo	Biscoe	46.2	14.5	209.0	4800.0	female	2007
Gentoo	Biscoe	48.7	15.1	222.0	5350.0	male	2007
Gentoo	Biscoe	50.2	14.3	218.0	5700.0	male	2007
Gentoo	Biscoe	45.1	14.5	215.0	5000.0	female	2007
Gentoo	Biscoe	46.5	14.5	213.0	4400.0	female	2007
Gentoo	Biscoe	46.3	15.8	215.0	5050.0	male	2007
Gentoo	Biscoe	42.9	13.1	215.0	5000.0	female	2007
Gentoo	Biscoe	46.1	15.1	215.0	5100.0	male	2007
Gentoo	Biscoe	44.5	14.3	216.0	4100.0	NaN	2007
Gentoo	Biscoe	47.8	15.0	215.0	5650.0	male	2007
Gentoo	Biscoe	48.2	14.3	210.0	4600.0	female	2007
Gentoo	Biscoe	50.0	15.3	220.0	5550.0	male	2007
Gentoo	Biscoe	47.3	15.3	222.0	5250.0	male	2007
Gentoo	Biscoe	42.8	14.2	209.0	4700.0	female	2007
Gentoo	Biscoe	45.1	14.5	207.0	5050.0	female	2007
Gentoo	Biscoe	59.6	17.0	230.0	6050.0	male	2007
Gentoo	Biscoe	49.1	14.8	220.0	5150.0	female	2008
Gentoo	Biscoe	48.4	16.3	220.0	5400.0	male	2008
Gentoo	Biscoe	42.6	13.7	213.0	4950.0	female	2008
Gentoo	Biscoe	44.4	17.3	219.0	5250.0	male	2008
Gentoo	Biscoe	44.0	13.6	208.0	4350.0	female	2008
Gentoo	Biscoe	48.7	15.7	208.0	5350.0	male	2008
Gentoo	Biscoe	42.7	13.7	208.0	3950.0	female	2008
Gentoo	Biscoe	49.6	16.0	225.0	5700.0	male	2008
Gentoo	Biscoe	45.3	13.7	210.0	4300.0	female	2008
Gentoo	Biscoe	49.6	15.0	216.0	4750.0	male	2008
Gentoo	Biscoe	50.5	15.9	222.0	5550.0	male	2008
Gentoo	Biscoe	43.6	13.9	217.0	4900.0	female	2008
Gentoo	Biscoe	45.5	13.9	210.0	4200.0	female	2008
Gentoo	Biscoe	50.5	15.9	225.0	5400.0	male	2008
Gentoo	Biscoe	44.9	13.3	213.0	5100.0	female	2008
Gentoo	Biscoe	45.2	15.8	215.0	5300.0	male	2008
Gentoo	Biscoe	46.6	14.2	210.0	4850.0	female	2008
Gentoo	Biscoe	48.5	14.1	220.0	5300.0	male	2008
Gentoo	Biscoe	45.1	14.4	210.0	4400.0	female	2008
Gentoo	Biscoe	50.1	15.0	225.0	5000.0	male	2008
Gentoo	Biscoe	46.5	14.4	217.0	4900.0	female	2008
Gentoo	Biscoe	45.0	15.4	220.0	5050.0	male	2008
Gentoo	Biscoe	43.8	13.9	208.0	4300.0	female	2008
Gentoo	Biscoe	45.5	15.0	220.0	5000.0	male	2008
Gentoo	Biscoe	43.2	14.5	208.0	4450.0	female	2008
Gentoo	Biscoe	50.4	15.3	224.0	5550.0	male	2008
Gentoo	Biscoe	45.3	13.8	208.0	4200.0	female	2008
Gentoo	Biscoe	46.2	14.9	221.0	5300.0	male	2008
Gentoo	Biscoe	45.7	13.9	214.0	4400.0	female	2008
Gentoo	Biscoe	54.3	15.7	231.0	5650.0	male	2008
Gentoo	Biscoe	45.8	14.2	219.0	4700.0	female	2008
Gentoo	Biscoe	49.8	16.8	230.0	5700.0	male	2008
Gentoo	Biscoe	46.2	14.4	214.0	4650.0	NaN	2008
Gentoo	Biscoe	49.5	16.2	229.0	5800.0	male	2008
Gentoo	Biscoe	43.5	14.2	220.0	4700.0	female	2008
Gentoo	Biscoe	50.7	15.0	223.0	5550.0	male	2008
Gentoo	Biscoe	47.7	15.0	216.0	4750.0	female	2008
Gentoo	Biscoe	46.4	15.6	221.0	5000.0	male	2008
Gentoo	Biscoe	48.2	15.6	221.0	5100.0	male	2008
Gentoo	Biscoe	46.5	14.8	217.0	5200.0	female	2008
Gentoo	Biscoe	46.4	15.0	216.0	4700.0	female	2008
Gentoo	Biscoe	48.6	16.0	230.0	5800.0	male	2008
Gentoo	Biscoe	47.5	14.2	209.0	4600.0	female	2008
Gentoo	Biscoe	51.1	16.3	220.0	6000.0	male	2008
Gentoo	Biscoe	45.2	13.8	215.0	4750.0	female	2008
Gentoo	Biscoe	45.2	16.4	223.0	5950.0	male	2008
Gentoo	Biscoe	49.1	14.5	212.0	4625.0	female	2009
Gentoo	Biscoe	52.5	15.6	221.0	5450.0	male	2009
Gentoo	Biscoe	47.4	14.6	212.0	4725.0	female	2009
Gentoo	Biscoe	50.0	15.9	224.0	5350.0	male	2009
Gentoo	Biscoe	44.9	13.8	212.0	4750.0	female	2009
Gentoo	Biscoe	50.8	17.3	228.0	5600.0	male	2009
Gentoo	Biscoe	43.4	14.4	218.0	4600.0	female	2009
Gentoo	Biscoe	51.3	14.2	218.0	5300.0	male	2009
Gentoo	Biscoe	47.5	14.0	212.0	4875.0	female	2009
Gentoo	Biscoe	52.1	17.0	230.0	5550.0	male	2009
Gentoo	Biscoe	47.5	15.0	218.0	4950.0	female	2009
Gentoo	Biscoe	52.2	17.1	228.0	5400.0	male	2009
Gentoo	Biscoe	45.5	14.5	212.0	4750.0	female	2009
Gentoo	Biscoe	49.5	16.1	224.0	5650.0	male	2009
Gentoo	Biscoe	44.5	14.7	214.0	4850.0	female	2009
Gentoo	Biscoe	50.8	15.7	226.0	5200.0	male	2009
Gentoo	Biscoe	49.4	15.8	216.0	4925.0	male	2009
Gentoo	Biscoe	46.9	14.6	222.0	4875.0	female	2009
Gentoo	Biscoe	48.4	14.4	203.0	4625.0	female	2009
Gentoo	Biscoe	51.1	16.5	225.0	5250.0	male	2009
Gentoo	Biscoe	48.5	15.0	219.0	4850.0	female	2009
Gentoo	Biscoe	55.9	17.0	228.0	5600.0	male	2009
Gentoo	Biscoe	47.2	15.5	215.0	4975.0	female	2009
Gentoo	Biscoe	49.1	15.0	228.0	5500.0	male	2009
Gentoo	Biscoe	47.3	13.8	216.0	4725.0	NaN	2009
Gentoo	Biscoe	46.8	16.1	215.0	5500.0	male	2009
Gentoo	Biscoe	41.7	14.7	210.0	4700.0	female	2009
Gentoo	Biscoe	53.4	15.8	219.0	5500.0	male	2009
Gentoo	Biscoe	43.3	14.0	208.0	4575.0	female	2009
Gentoo	Biscoe	48.1	15.1	209.0	5500.0	male	2009
Gentoo	Biscoe	50.5	15.2	216.0	5000.0	female	2009
Gentoo	Biscoe	49.8	15.9	229.0	5950.0	male	2009
Gentoo	Biscoe	43.5	15.2	213.0	4650.0	female	2009
Gentoo	Biscoe	51.5	16.3	230.0	5500.0	male	2009
Gentoo	Biscoe	46.2	14.1	217.0	4375.0	female	2009
Gentoo	Biscoe	55.1	16.0	230.0	5850.0	male	2009
Gentoo	Biscoe	44.5	15.7	217.0	4875.0	NaN	2009
Gentoo	Biscoe	48.8	16.2	222.0	6000.0	male	2009
Gentoo	Biscoe	47.2	13.7	214.0	4925.0	female	2009
Gentoo	Biscoe	NaN	NaN	NaN	NaN	NaN	2009
Gentoo	Biscoe	46.8	14.3	215.0	4850.0	female	2009
Gentoo	Biscoe	50.4	15.7	222.0	5750.0	male	2009
Gentoo	Biscoe	45.2	14.8	212.0	5200.0	female	2009
Gentoo	Biscoe	49.9	16.1	213.0	5400.0	male	2009
Chinstrap	Dream	46.5	17.9	192.0	3500.0	female	2007
Chinstrap	Dream	50.0	19.5	196.0	3900.0	male	2007
Chinstrap	Dream	51.3	19.2	193.0	3650.0	male	2007
Chinstrap	Dream	45.4	18.7	188.0	3525.0	female	2007
Chinstrap	Dream	52.7	19.8	197.0	3725.0	male	2007
Chinstrap	Dream	45.2	17.8	198.0	3950.0	female	2007
Chinstrap	Dream	46.1	18.2	178.0	3250.0	female	2007
Chinstrap	Dream	51.3	18.2	197.0	3750.0	male	2007
Chinstrap	Dream	46.0	18.9	195.0	4150.0	female	2007
Chinstrap	Dream	51.3	19.9	198.0	3700.0	male	2007
Chinstrap	Dream	46.6	17.8	193.0	3800.0	female	2007
Chinstrap	Dream	51.7	20.3	194.0	3775.0	male	2007
Chinstrap	Dream	47.0	17.3	185.0	3700.0	female	2007
Chinstrap	Dream	52.0	18.1	201.0	4050.0	male	2007
Chinstrap	Dream	45.9	17.1	190.0	3575.0	female	2007
Chinstrap	Dream	50.5	19.6	201.0	4050.0	male	2007
Chinstrap	Dream	50.3	20.0	197.0	3300.0	male	2007
Chinstrap	Dream	58.0	17.8	181.0	3700.0	female	2007
Chinstrap	Dream	46.4	18.6	190.0	3450.0	female	2007
Chinstrap	Dream	49.2	18.2	195.0	4400.0	male	2007
Chinstrap	Dream	42.4	17.3	181.0	3600.0	female	2007
Chinstrap	Dream	48.5	17.5	191.0	3400.0	male	2007
Chinstrap	Dream	43.2	16.6	187.0	2900.0	female	2007
Chinstrap	Dream	50.6	19.4	193.0	3800.0	male	2007
Chinstrap	Dream	46.7	17.9	195.0	3300.0	female	2007
Chinstrap	Dream	52.0	19.0	197.0	4150.0	male	2007
Chinstrap	Dream	50.5	18.4	200.0	3400.0	female	2008
Chinstrap	Dream	49.5	19.0	200.0	3800.0	male	2008
Chinstrap	Dream	46.4	17.8	191.0	3700.0	female	2008
Chinstrap	Dream	52.8	20.0	205.0	4550.0	male	2008
Chinstrap	Dream	40.9	16.6	187.0	3200.0	female	2008
Chinstrap	Dream	54.2	20.8	201.0	4300.0	male	2008
Chinstrap	Dream	42.5	16.7	187.0	3350.0	female	2008
Chinstrap	Dream	51.0	18.8	203.0	4100.0	male	2008
Chinstrap	Dream	49.7	18.6	195.0	3600.0	male	2008
Chinstrap	Dream	47.5	16.8	199.0	3900.0	female	2008
Chinstrap	Dream	47.6	18.3	195.0	3850.0	female	2008
Chinstrap	Dream	52.0	20.7	210.0	4800.0	male	2008
Chinstrap	Dream	46.9	16.6	192.0	2700.0	female	2008
Chinstrap	Dream	53.5	19.9	205.0	4500.0	male	2008
Chinstrap	Dream	49.0	19.5	210.0	3950.0	male	2008
Chinstrap	Dream	46.2	17.5	187.0	3650.0	female	2008
Chinstrap	Dream	50.9	19.1	196.0	3550.0	male	2008
Chinstrap	Dream	45.5	17.0	196.0	3500.0	female	2008
Chinstrap	Dream	50.9	17.9	196.0	3675.0	female	2009
Chinstrap	Dream	50.8	18.5	201.0	4450.0	male	2009
Chinstrap	Dream	50.1	17.9	190.0	3400.0	female	2009
Chinstrap	Dream	49.0	19.6	212.0	4300.0	male	2009
Chinstrap	Dream	51.5	18.7	187.0	3250.0	male	2009
Chinstrap	Dream	49.8	17.3	198.0	3675.0	female	2009
Chinstrap	Dream	48.1	16.4	199.0	3325.0	female	2009
Chinstrap	Dream	51.4	19.0	201.0	3950.0	male	2009
Chinstrap	Dream	45.7	17.3	193.0	3600.0	female	2009
Chinstrap	Dream	50.7	19.7	203.0	4050.0	male	2009
Chinstrap	Dream	42.5	17.3	187.0	3350.0	female	2009
Chinstrap	Dream	52.2	18.8	197.0	3450.0	male	2009
Chinstrap	Dream	45.2	16.6	191.0	3250.0	female	2009
Chinstrap	Dream	49.3	19.9	203.0	4050.0	male	2009
Chinstrap	Dream	50.2	18.8	202.0	3800.0	male	2009
Chinstrap	Dream	45.6	19.4	194.0	3525.0	female	2009
Chinstrap	Dream	51.9	19.5	206.0	3950.0	male	2009
Chinstrap	Dream	46.8	16.5	189.0	3650.0	female	2009
Chinstrap	Dream	45.7	17.0	195.0	3650.0	female	2009
Chinstrap	Dream	55.8	19.8	207.0	4000.0	male	2009
Chinstrap	Dream	43.5	18.1	202.0	3400.0	female	2009
Chinstrap	Dream	49.6	18.2	193.0	3775.0	male	2009
Chinstrap	Dream	50.8	19.0	210.0	4100.0	male	2009
Chinstrap	Dream	50.2	18.7	198.0	3775.0	female	2009

Tables from code

If you want fancier tables, try the great_tables package and all that it offers!

import great_tables as gt

(
    gt.GT(penguins.head())
    .tab_style(
        style = [
            gt.style.fill(color = "pink"),
            gt.style.text(weight = "italic")
        ],
        locations = gt.loc.body(
          columns= "bill_length_mm",
          rows = lambda x: x["bill_length_mm"] > 40
        )
    )
)

species	island	bill_length_mm	bill_depth_mm	flipper_length_mm	body_mass_g	sex	year
Adelie	Torgersen	39.1	18.7	181.0	3750.0	male	2007
Adelie	Torgersen	39.5	17.4	186.0	3800.0	female	2007
Adelie	Torgersen	40.3	18.0	195.0	3250.0	female	2007
Adelie	Torgersen						2007
Adelie	Torgersen	36.7	19.3	193.0	3450.0	female	2007

Figures

Markdown figures

Markdown syntax:

![Penguins playing with a Quarto ball](images/penguins-quarto-ball.png)

Output:

Penguins playing with a Quarto ball

Markdown figures with options

Markdown syntax:

![Penguins playing with a Quarto ball](images/penguins-quarto-ball.png){fig-align="left"}

Output:

Penguins playing with a Quarto ball

Markdown figures with options

Markdown syntax:

![](images/penguins-quarto-ball.png){height="100px" fig-alt="Illustration of two penguins playing with a Quarto ball."}

Output:

Illustration of two penguins playing with a Quarto ball.

Subfigures

Markdown syntax:

::: {#fig-penguins layout-ncol=2}

![Blue penguin](images/blue-penguin.png){#fig-blue height="150px"}

![Orange penguin](images/orange-penguin.png){#fig-orange height="150px"}

Two penguins
:::

Output:

Figure divs

Markdown syntax:

::: {#fig-penguin}
<iframe width="420" height="237" src="https://www.youtube.com/embed/q3uXXh1sHcI"></iframe>

Baby penguin tries to make friends
:::

Output:

Figure 2: Baby penguin tries to make friends

Figures from code

```{python}
import plotnine as p9

(
  p9.ggplot(penguins, p9.aes(x = "species", fill = "species")) 
  + p9.geom_bar(show_legend = None)
)
```

Cross references

Help readers to navigate your document with numbered references and hyperlinks to entities like figures and tables.
Cross referencing steps:
- Add a caption to your figure or table.
- Give an id to your figure or table, starting with fig- or tbl-.
- Refer to it with @fig-... or @tbl-....

Figure cross references

The presence of the caption (Blue penguin) and label (#fig-blue-penguin) make this figure referenceable:

Markdown syntax:

See @fig-blue-penguin for a cute blue penguin.

![Blue penguin](images/blue-penguin.png){#fig-blue-penguin height=200px}

Output:

See Figure 3 for a cute blue penguin.

Table cross references

The presence of the caption (A few penguins) and label (#tbl-penguins) make this table referenceable:

Markdown syntax:

See @tbl-penguins for data on a few penguins.

```{python}
#| label: tbl-penguins
#| tbl-cap: A few penguins
gt.GT(penguins.head())
```

Output:

See Table 1 for data on a few penguins.

gt.GT(penguins.head())

Table 1: A few penguins

species	island	bill_length_mm	bill_depth_mm	flipper_length_mm	body_mass_g	sex	year
Adelie	Torgersen	39.1	18.7	181.0	3750.0	male	2007
Adelie	Torgersen	39.5	17.4	186.0	3800.0	female	2007
Adelie	Torgersen	40.3	18.0	195.0	3250.0	female	2007
Adelie	Torgersen						2007
Adelie	Torgersen	36.7	19.3	193.0	3450.0	female	2007

Your turn

Open tables-figures.qmd.
Follow the instructions in the document, then exchange one new thing you’ve learned with your neighbor.

10:00

Wrap up

Learn more

quarto.org/docs/guide > Documents

Questions

Any questions / anything you’d like to review before we wrap up this module?

Documents

Anatomy of a Quarto document

Components

Literate programming

Metadata

YAML

Output options

Output option arguments

YAML validation

YAML validation

Why YAML?

Quarto linting

Quarto YAML Intelligence

Your turn

List of valid YAML fields

Text

TL;DR

Text Formatting

Headings

Header 1

Header 2

Header 3

Header 4

Header 5

Header 6

Links

Lists

Quotes

Divs

Divs with pre-defined classes

Spans

Your turn

Callouts

More callouts

Your turn

Footnotes

Inline footnotes

Numbered footnotes

Code

Anatomy of a code chunk

Code, who is it for?

Code

Showing and hiding code with echo

Tables and figures

Tables

Markdown tables

Grid tables

Grid tables: Alignment

Grid tables: Authoring

Tables from code

Tables from code

Figures

Markdown figures

Markdown figures with options

Markdown figures with options

Subfigures

Figure divs

Figures from code

Cross references

Cross references

Figure cross references

Table cross references

Your turn

Wrap up

Learn more

Questions

Showing and hiding code with `echo`