grouped_violin_plots.qmd

# Grouped violin plots {#sec-grouped-violin-plots}

```{r}
#| label: setup
#| message: false
#| warning: false
#| include: false
library(tidyverse)
library(lubridate)
library(scales)
library(knitr)
library(kableExtra)
library(colorblindr)
library(downlit)
# fonts ----
library(extrafont)
library(sysfonts)
source("_common.R")
# use font
showtext::showtext_auto()
# set theme
ggplot2::theme_set(theme_ggp2g(
    base_size = 15))
```

```{r}
#| label: status
#| results: "asis"
#| echo: false
# status ----
# polish, dev, draft, complete
status("complete")
```

:::: {.callout-note collapse="false" icon=false}

<br>

```{r}
#| label: full_code_display
#| eval: true
#| echo: false
#| warning: false
#| message: false
#| out-height: '60%'
#| out-width: '60%'
#| fig-align: right
library(palmerpenguins) 
library(ggplot2)
peng_violin <- filter(penguins, !is.na(island))
labs_grp_violin <- labs(
  title = "Adult foraging penguins", 
  subtitle = "Palmer Archipelago, Antarctica",
  x = "Island", fill = "Island",
  y = "Bill length (millimeters)")
ggp2_grp_violin <- ggplot(data = peng_violin,
       aes(x = island, 
           y = bill_length_mm, 
        fill = island)) +
  geom_violin(alpha = 2/3, 
      show.legend = FALSE) 
ggp2_grp_violin + 
  labs_grp_violin
```

::: {style="font-size: 1.10em; color: #02577A;"}
**This graph requires:**
:::

::: {style="font-size: 1.05em; color: #282b2d;"}
**`r emo::ji("check")` a categorical variable**      
:::

::: {style="font-size: 1.05em; color: #282b2d;"}
**`r emo::ji("check")` a numeric (continuous) variable**
:::

::::

## Description 

A ‘violin plot’ is a variation of a density or ridgeline plot,  where the distribution is plotted symmetrically, creating a two-sided, smoothed distribution.

## Set up

::: {style="font-size: 1.15em; color: #1e83c8;"}
**PACKAGES:**
:::

::: {style="font-size: 0.95rem;"}
Install packages.
:::


::: {style="font-size: 0.85em;"}
```{r}
#| label: pkg_code_grp_violin
#| code-fold: show
#| eval: false
#| echo: true
#| warning: false
#| message: false
#| results: hide
install.packages("palmerpenguins")
library(palmerpenguins)
library(ggplot2)
```
:::



::: {style="font-size: 1.15em; color: #1e83c8;"}
**DATA:**
:::

::: {.column-margin}
![Artwork by allison horst](www/lter_penguins.png){fig-align="right" width="100%" height="100%"}
:::

::: {style="font-size: 0.95rem;"}
Remove missing `island` from `penguins`
:::

::: {style="font-size: 0.85em;"}
```{r}
#| label: data_code_grp_violin
#| code-fold: show
#| eval: true
#| echo: true
peng_violin <- filter(penguins, !is.na(island))
glimpse(peng_violin)
```
:::


::: {style="font-size: 1.15em; color: #1e83c8;"}
**CODE:**
:::

  -   Create labels with `labs()`

  -   Initialize the graph with `ggplot()` and provide `data`

  -   Map `island` to the `x`, `bill_length_mm` to the `y`, and  `island` to `fill` 

  -   Set `alpha` to `2/3`

  -   Remove the legend with `show.legend = FALSE`

::: {style="font-size: 0.85em;"}
```{r}
#| label: code_graph_grp_violin
#| code-fold: show
#| eval: false
#| echo: true 
#| warning: false
#| message: false
#| out-height: '100%'
#| out-width: '100%'
labs_grp_violin <- labs(
  title = "Adult foraging penguins", 
  subtitle = "Palmer Archipelago, Antarctica",
  x = "Island", fill = "Island",
  y = "Bill length (millimeters)")
ggp2_grp_violin <- ggplot(data = peng_violin,
       aes(x = island, 
           y = bill_length_mm, 
        fill = island)) +
  geom_violin(alpha = 2/3, 
      show.legend = FALSE) 
ggp2_grp_violin + 
  labs_grp_violin
```
:::



::: {style="font-size: 1.15em; color: #1e83c8;"}
**GRAPH:**
:::


Violin plots can allow us to compare the 'center' and 'spread' of continuous variables across categorical groups.

::: {style="font-size: 0.85em;"}
```{r}
#| label: create_graph_grp_violin
#| eval: true
#| echo: true
#| warning: false
#| message: false
#| out-height: '100%'
#| out-width: '100%'
#| layout-nrow: 1
#| column: page-inset-right
labs_grp_violin <- labs(
  title = "Adult foraging penguins", 
  subtitle = "Palmer Archipelago, Antarctica",
  x = "Island", fill = "Island",
  y = "Bill length (millimeters)")
ggp2_grp_violin <- ggplot(data = peng_violin,
       aes(x = island, 
           y = bill_length_mm, 
        fill = island)) +
  geom_violin(alpha = 2/3, 
      show.legend = FALSE) 
ggp2_grp_violin + 
  labs_grp_violin
```
:::

## More info

### Quartiles

::: {.column-margin}
Change the shape of the line with [`linetype` and `linewidth`](https://ggplot2.tidyverse.org/reference/geom_violin.html#aesthetics).
:::


We can include lines for the 25th, 50th, and 75th quartiles using the `draw_quantiles` argument. 

::: {style="font-size: 0.85em;"}
```{r}
#| label: grp_violin_draw_quantiles
#| eval: true
#| echo: true
#| warning: false
#| message: false
#| out-height: '100%'
#| out-width: '100%'
#| layout-nrow: 1
#| column: page-inset-right
ggplot(data = peng_violin,
       aes(x = island, 
           y = bill_length_mm, 
        fill = island)) +
  geom_violin(
      draw_quantiles = c(0.25, 0.5, 0.75),
      alpha = 1/2, 
      linewidth = 0.5, 
      show.legend = FALSE) 
```
:::

### Kernel


The [`kernel` argument](https://ggplot2.tidyverse.org/reference/geom_violin.html#arguments) let's us change the "*kernel density estimate*" used to create the violin shape. The possible [kernel density estimates](https://stat.ethz.ch/R-manual/R-devel/library/stats/html/density.html) are `"gaussian"`, `"epanechnikov"`, `"rectangular"`, `"triangular"`, `"biweight"`, `"cosine"`, and `"optcosine"` 

::: {style="font-size: 0.85em;"}
```{r}
#| label: grp_violin_kernel
#| eval: true
#| echo: true
#| warning: false
#| message: false
#| out-height: '100%'
#| out-width: '100%'
#| layout-nrow: 1
#| column: page-inset-right
ggplot(data = peng_violin,
       aes(x = island, 
           y = bill_length_mm, 
        fill = island)) +
  geom_violin(alpha = 1/2, 
      linewidth = 0.5, 
      kernel = "rectangular",
      show.legend = FALSE) 
```
:::

### Bandwidth


We can directly adjust the shape of the violin with the [`bw` argument](https://ggplot2.tidyverse.org/reference/geom_violin.html#arguments), which is the *standard deviation of the smoothing kernel.* The [`trim` argument](https://ggplot2.tidyverse.org/reference/geom_violin.html#arguments) *trim(s) the tails of the violins to the range of the data.*

::: {style="font-size: 0.85em;"}
```{r}
#| label: grp_violin_bw
#| eval: true
#| echo: true
#| warning: false
#| message: false
#| out-height: '100%'
#| out-width: '100%'
#| layout-nrow: 1
#| column: page-inset-right
# bw of 0.5
grp_violin_bw0p5 <- ggplot(data = peng_violin,
       aes(x = island, 
           y = bill_length_mm, 
        fill = island)) +
  geom_violin(bw = 0.5, 
      alpha = 2/3, 
      trim = TRUE,
      show.legend = FALSE) 
grp_violin_bw0p5 + 
    labs_grp_violin + 
    labs(caption = "bw = 0.5")
# bw of 4.5
grp_violin_bw4p5 <- ggplot(data = peng_violin,
       aes(x = island, 
           y = bill_length_mm, 
        fill = island)) +
  geom_violin(bw = 4.5, 
      alpha = 2/3, 
      trim = TRUE,
      show.legend = FALSE) 
grp_violin_bw4p5 + 
    labs_grp_violin + 
    labs(caption = "bw = 4.5")
```
:::