codemix.qmd

# Mixing multiple languages in the same chapter

This is a book created from markdown and executable code.

See @knuth84 for additional discussion of literate programming.

## Running Python code

For a demonstration of a line plot on a polar axis, see @fig-polar.

```{python}
#| label: fig-polar-2
#| fig-cap: "A line plot on a polar axis"

import numpy as np
import matplotlib.pyplot as plt

r = np.arange(0, 2, 0.01)
theta = 2 * np.pi * r
fig, ax = plt.subplots(
  subplot_kw = {'projection': 'polar'} 
)
ax.plot(theta, r)
ax.set_rticks([0.5, 1, 1.5, 2])
ax.grid(True)
plt.show()
```

## Running R code

```{r}
library(palmerpenguins)
library(ggplot2)
ggplot2::theme_set(ggplot2::theme_minimal())
```

## Example graph using penguins dataset

```{r}
#| label: fig-penguins
#| fig-cap: "Flipper length and body mass for Adelie, Chinstrap and Gentoo Penguins"
#| warning: false

mass_flipper <- ggplot(data = penguins, 
                       aes(x = flipper_length_mm,
                           y = body_mass_g)) +
  geom_point(aes(color = species, 
                 shape = species),
             size = 3,
             alpha = 0.8) +
  scale_color_manual(values = c("darkorange","purple","cyan4")) +
  labs(title = "Penguin size, Palmer Station LTER",
       subtitle = "Flipper length vs. body mass",
       x = "Flipper length (mm)",
       y = "Body mass (g)",
       color = "Penguin species",
       shape = "Penguin species") +
  theme(legend.position = c(0.2, 0.7),
        plot.title.position = "plot",
        plot.caption = element_text(hjust = 0, face= "italic"),
        plot.caption.position = "plot")

mass_flipper
```