Reproducible Documentation with Quarto

1 Set up

1. Install Python on your machine.

2. Install Quarto

3. Go to cmd and type

   • py --version

   • py -m pip install pandas plotly statsmodels

   • py -m pip install palmerpenguins

   • py -m pip install plotnine

   Note: The reason for typing py -m instead of just pip install is to avoid issues where you might have multiple versions of Python installed, and pip could be tied to the wrong version. By running py -m pip, you’re explicitly telling the Python launcher to use the right Python interpreter and its associated pip.

2 Loading packages

import pandas as pd
import plotnine as p9 
from plotnine import ggplot, geom_point, aes, stat_smooth, facet_wrap, labs
from palmerpenguins import load_penguins

3 Data

penguins = load_penguins()
penguins.head()

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

4 Data Visualisation with plotnine

4.1 Step 1: Take data and obtain a canvas for plotting

ggplot(penguins)

4.2 Step 2: Defining Aesthetics

ggplot(penguins, aes("bill_length_mm", "bill_depth_mm", color="factor(species)"))

4.3 Step 3: Add Gemetries

ggplot(penguins, aes("bill_length_mm", "bill_depth_mm", color="factor(species)")) +  geom_point()

C:\Users\DELL\AppData\Local\Programs\Python\Python312\Lib\site-packages\plotnine\layer.py:364: PlotnineWarning: geom_point : Removed 2 rows containing missing values.

4.4 Step 4: Create the plot with customized axis labels

ggplot(penguins, aes("bill_length_mm", "bill_depth_mm", color="factor(species)")) +  geom_point()  + labs(x="Bill Length (mm)", y="Bill Depth (mm)")

C:\Users\DELL\AppData\Local\Programs\Python\Python312\Lib\site-packages\plotnine\layer.py:364: PlotnineWarning: geom_point : Removed 2 rows containing missing values.

5 Change themes

5.1 Without customized themes

p9.ggplot(data=penguins,
           mapping=p9.aes(x='factor(species)')) + p9.geom_bar() 

5.2 With customized themes

p9.ggplot(data=penguins,
           mapping=p9.aes(x='factor(species)')) + p9.geom_bar() + p9.theme_bw() + p9.theme(axis_text_x = p9.element_text(angle=90))

6 Faceting

6.1 Without faceting

ggplot(penguins, aes("bill_length_mm", "bill_depth_mm", color="factor(species)")) +  geom_point()  + labs(x="Bill Length (mm)", y="Bill Depth (mm)") 

C:\Users\DELL\AppData\Local\Programs\Python\Python312\Lib\site-packages\plotnine\layer.py:364: PlotnineWarning: geom_point : Removed 2 rows containing missing values.

6.2 With faceting

ggplot(penguins, aes("bill_length_mm", "bill_depth_mm", color="factor(species)")) +  geom_point()  + labs(x="Bill Length (mm)", y="Bill Depth (mm)") + facet_wrap("species")

C:\Users\DELL\AppData\Local\Programs\Python\Python312\Lib\site-packages\plotnine\layer.py:364: PlotnineWarning: geom_point : Removed 2 rows containing missing values.

7 Other geoms

7.1 geom_boxplot

p9.ggplot(data=penguins,
           mapping=p9.aes(x='factor(species)', y='bill_length_mm')) + p9.geom_boxplot()

C:\Users\DELL\AppData\Local\Programs\Python\Python312\Lib\site-packages\plotnine\layer.py:284: PlotnineWarning: stat_boxplot : Removed 2 rows containing non-finite values.

7.2 geom_jitter

p9.ggplot(data=penguins,
           mapping=p9.aes(x='factor(species)', y='bill_length_mm')) + p9.geom_jitter()

C:\Users\DELL\AppData\Local\Programs\Python\Python312\Lib\site-packages\plotnine\layer.py:364: PlotnineWarning: geom_jitter : Removed 2 rows containing missing values.

7.3 geom_boxplot + geom_jitter

p9.ggplot(data=penguins,
           mapping=p9.aes(x='factor(species)', y='bill_length_mm', color='factor(species)')) + p9.geom_boxplot()+ p9.geom_jitter()

C:\Users\DELL\AppData\Local\Programs\Python\Python312\Lib\site-packages\plotnine\layer.py:284: PlotnineWarning: stat_boxplot : Removed 2 rows containing non-finite values.
C:\Users\DELL\AppData\Local\Programs\Python\Python312\Lib\site-packages\plotnine\layer.py:364: PlotnineWarning: geom_jitter : Removed 2 rows containing missing values.

7.4 To remove outliers from the boxplot in your ggplot code

p9.ggplot(data=penguins,
           mapping=p9.aes(x='factor(species)', y='bill_length_mm', color='factor(species)')) + p9.geom_boxplot(outlier_shape = "None")+ p9.geom_jitter()

C:\Users\DELL\AppData\Local\Programs\Python\Python312\Lib\site-packages\plotnine\layer.py:284: PlotnineWarning: stat_boxplot : Removed 2 rows containing non-finite values.
C:\Users\DELL\AppData\Local\Programs\Python\Python312\Lib\site-packages\plotnine\layer.py:364: PlotnineWarning: geom_jitter : Removed 2 rows containing missing values.

8 Working with chunk options

8.1 echo: false

C:\Users\DELL\AppData\Local\Programs\Python\Python312\Lib\site-packages\plotnine\layer.py:284: PlotnineWarning: stat_boxplot : Removed 2 rows containing non-finite values.
C:\Users\DELL\AppData\Local\Programs\Python\Python312\Lib\site-packages\plotnine\layer.py:364: PlotnineWarning: geom_jitter : Removed 2 rows containing missing values.

8.2 fig-cap

C:\Users\DELL\AppData\Local\Programs\Python\Python312\Lib\site-packages\plotnine\layer.py:284: PlotnineWarning: stat_boxplot : Removed 2 rows containing non-finite values.
C:\Users\DELL\AppData\Local\Programs\Python\Python312\Lib\site-packages\plotnine\layer.py:364: PlotnineWarning: geom_jitter : Removed 2 rows containing missing values.

Distribution of Bill length by Species

8.3 fig width

C:\Users\DELL\AppData\Local\Programs\Python\Python312\Lib\site-packages\plotnine\layer.py:284: PlotnineWarning: stat_boxplot : Removed 2 rows containing non-finite values.
C:\Users\DELL\AppData\Local\Programs\Python\Python312\Lib\site-packages\plotnine\layer.py:364: PlotnineWarning: geom_jitter : Removed 2 rows containing missing values.

Distribution of Bill length by Species

8.4 Suprress warnings and messages

Distribution of Bill length by Species

8.5 Fenced Echo

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

2

1 + 1

2

8.6 output and code-overflow

```{python}
#| output: false
#| code-overflow: wrap
1 + 1
```

1 + 1

9 Highlighting

1 + 1

10 Themes

format:
  html:
    theme: united

format:
  html: 
    theme: cosmo
    fontsize: 1.1em
    linestretch: 1.7

format:
  html: 
    theme: darkly

11 Folding Code

p9.ggplot(data=penguins,
           mapping=p9.aes(x='factor(species)', y='bill_length_mm', color='factor(species)')) + p9.geom_boxplot()

C:\Users\DELL\AppData\Local\Programs\Python\Python312\Lib\site-packages\plotnine\layer.py:284: PlotnineWarning: stat_boxplot : Removed 2 rows containing non-finite values.

12 Folding Code with code-summary

p9.ggplot(data=penguins,
           mapping=p9.aes(x='factor(species)', y='bill_length_mm', color='factor(species)')) + p9.geom_boxplot()

C:\Users\DELL\AppData\Local\Programs\Python\Python312\Lib\site-packages\plotnine\layer.py:284: PlotnineWarning: stat_boxplot : Removed 2 rows containing non-finite values.

13 Code-overflow

p9.ggplot(data=penguins,
           mapping=p9.aes(x='factor(species)', y='bill_length_mm', color='factor(species)')) + p9.geom_boxplot()

C:\Users\DELL\AppData\Local\Programs\Python\Python312\Lib\site-packages\plotnine\layer.py:284: PlotnineWarning: stat_boxplot : Removed 2 rows containing non-finite values.

14 Table of content

toc: true
toc-depth: 2

15 Title banner

title-block-banner: true

16 Word document output

format:
  docx:
    number-sections: true
    number-offset: 2
    number-depth: 3
    highlight-style: github