hex_bins.qmd

# Hexagon bins {#sec-hex-bins}

```{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 = 14))
```

```{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)
penguins_hex <- palmerpenguins::penguins |> 
    dplyr::select(flipper_length_mm, bill_depth_mm,
        bill_length_mm, species, sex, island) |> 
    tidyr::drop_na()
labs_hex <- labs(
    title = "Adult Foraging Penguins", 
    subtitle = "Near Palmer Station, Antarctica", 
    x = "Bill length (mm)", 
    y = "Flipper length (mm)")
ggp2_hex_b15 <- ggplot(data = penguins_hex,
    aes(x = bill_length_mm, y = flipper_length_mm)) +
    geom_hex(bins = 15)

ggp2_hex_b15 +
    labs_hex
```

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

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

::::

## Description 

Hexagon bins (or hex-bins) are a very similar to 2-D histograms, but instead of dividing the graph area into a grid, it's divided into hexagons. The number of points inside each per hexagon determine it's color. 


## Set up


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

Install packages.

::: {style="font-size: 0.85em;"}
```{r}
#| label: pkg_code_hex
#| 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%"}
:::



We'll take the `flipper_length_mm`, `bill_length_mm`, `bill_depth_mm`, `species`, `sex`, and `island` variables from `palmerpenguins::penguins` and drop the missing values.

::: {style="font-size: 0.85em;"}
```{r}
#| label: data_code_hex
#| code-fold: show
#| eval: true
#| echo: true
penguins_hex <- palmerpenguins::penguins |> 
    dplyr::select(flipper_length_mm, bill_depth_mm,
        bill_length_mm, species, sex, island) |> 
    tidyr::drop_na()
glimpse(penguins_hex)
```
:::

## Grammar

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

  - Create labels with `labs()`

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

  - Map `bill_length_mm` to the `x` and `flipper_length_mm` to the `y`

  - Add the `geom_hex()` layer

::: {style="font-size: 0.85em;"}
```{r}
#| label: code_graph_hex
#| code-fold: show
#| eval: false
#| echo: true 
#| warning: false
#| message: false
#| out-height: '100%'
#| out-width: '100%'
labs_hex <- labs(
    title = "Adult Foraging Penguins", 
    subtitle = "Near Palmer Station, Antarctica", 
    x = "Bill length (mm)", 
    y = "Flipper length (mm)")
# graph
ggp2_hex <- ggplot(data = penguins_hex, 
    aes(x = bill_length_mm, y = flipper_length_mm)) + 
    geom_hex()

ggp2_hex + 
    labs_hex
```
:::

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

::: {style="font-size: 0.85em;"}
```{r}
#| label: create_graph_hex
#| eval: true
#| echo: false
#| warning: false
#| message: false
#| out-height: '100%'
#| out-width: '100%'
#| layout-nrow: 1
#| column: page-inset-right
labs_hex <- labs(
    title = "Adult Foraging Penguins",
    subtitle = "Near Palmer Station, Antarctica",
    x = "Bill length (mm)",
    y = "Flipper length (mm)")
# graph
ggp2_hex <- ggplot(data = penguins_hex,
    aes(x = bill_length_mm, y = flipper_length_mm)) +
    geom_hex()

ggp2_hex +
    labs_hex
```
:::

## More info

### Bins

Below we change the `bins` to `20` and `15` and save these layers as `ggp2_hex_b20` and `ggp2_hex_b15`.

*Decreasing* the number of `bins` *increases* the size of the hexagons (and makes them larger). 

::: {style="font-size: 0.85em;"}
```{r}
#| label: bins_hex
#| eval: true
#| echo: true
#| warning: false
#| message: false
#| out-height: '100%'
#| out-width: '100%'
#| layout-nrow: 1
#| column: page-inset-right
ggp2_hex_b20 <- ggplot(data = penguins_hex,
    aes(x = bill_length_mm, y = flipper_length_mm)) +
    geom_hex(bins = 20)
ggp2_hex_b20 +
    labs_hex


ggp2_hex_b15 <- ggplot(data = penguins_hex,
    aes(x = bill_length_mm, y = flipper_length_mm)) +
    geom_hex(bins = 15)
ggp2_hex_b15 +
    labs_hex
```

:::

### Scale

  - We can adjust the color scale using  `scale_color_discrete_sequential()` and setting `aesthetics` to `"fill"`. 

  - If the hexagons overlap, we can use the `alpha` to make them slightly transparent. 

::: {style="font-size: 0.85em;"}
```{r}
#| label: scales_2d_hex
#| eval: true
#| echo: true
#| warning: false
#| message: false
#| out-height: '100%'
#| out-width: '100%'
#| layout-nrow: 1
#| column: page-inset-right
labs_hex2 <- labs(
    title = "Adult Foraging Penguins", 
    subtitle = "Near Palmer Station, Antarctica", 
    x = "Bill length (mm)", 
    y = "Flipper length (mm)",
    fill = "Sex")
ggplot(data = penguins_hex, 
    aes(x = bill_length_mm, 
        y = flipper_length_mm)) + 
    geom_hex(aes(fill = sex), 
             bins = 15, 
             alpha = 3/4) + 
    scale_color_discrete_sequential(
        aesthetics = "fill", 
        rev = FALSE,
        palette = "Viridis") +
    labs_hex2
```
:::

Get a full list of available color palette's using `hcl_palettes(type = ` `"sequential")`

### Options

  - `binwidth` allows us to manually adjust the size of the hexagons.

  - `linewidth` is also helpful when using `alpha` for overlapping values. 

::: {style="font-size: 0.85em;"}
```{r}
#| label: pals_2d_hex
#| eval: true
#| echo: true
#| warning: false
#| message: false
#| out-height: '100%'
#| out-width: '100%'
#| layout-nrow: 1
#| column: page-inset-right
labs_hex3 <- labs(
    title = "Adult Foraging Penguins", 
    subtitle = "Near Palmer Station, Antarctica", 
    x = "Bill length (mm)", 
    y = "Flipper length (mm)",
    fill = "Species")

ggplot(data = penguins_hex, 
    aes(x = bill_length_mm, 
        y = flipper_length_mm, 
        fill = species)) + 
    geom_hex(binwidth = c(1.1, 3),
        linewidth = 0.5, 
        alpha = 3/4,
        color = "#000000") + 
    scale_color_discrete_sequential(
        aesthetics = "fill", 
        palette = "Dark Mint") +
    labs_hex3
```
:::


Bins can be set with `bins` (a single number) or `binwidth` (a numeric vector of `c(x, y)`)