### Install ggprism from GitHub

Source: https://github.com/csdaw/ggprism/blob/master/README.md

Use this command to install the development version of the ggprism package directly from GitHub. Ensure the 'remotes' package is installed.

```r
remotes::install_github("csdaw/ggprism")
```

--------------------------------

### Bracket Axis Guide for Discrete Axes

Source: https://context7.com/csdaw/ggprism/llms.txt

Illustrates the use of guide_prism_bracket for discrete axes, replacing standard ticks with bracket glyphs around labels. This guide is particularly effective for emphasizing categories on discrete scales.

```r
base + scale_x_discrete(guide = "prism_bracket")
```

```r
base + guides(x = "prism_bracket")
```

```r
base + scale_x_discrete(guide = guide_prism_bracket(width = 0.12))
```

```r
base + scale_x_discrete(guide = guide_prism_bracket(width = 0.12, outside = FALSE))
```

```r
base + scale_x_discrete(guide = "prism_bracket") + coord_flip()
```

```r
base + scale_x_discrete(guide = guide_prism_bracket(width = 0.12)) + theme(axis.line.x = element_line(colour = "red"), axis.ticks.x = element_line(colour = "blue"), axis.text.x = element_text(colour = "darkgreen"))
```

--------------------------------

### Offset Axis Guide with Custom Limits and Breaks

Source: https://context7.com/csdaw/ggprism/llms.txt

Demonstrates using the prism_offset guide for continuous axes with custom limits and breaks. This guide creates an axis line that only appears between the outermost ticks.

```r
base + guides(x = "prism_offset", y = "prism_offset") + scale_x_continuous(limits = c(1, 6), breaks = seq(1, 6, by = 1))
```

```r
base + scale_x_continuous(limits = c(0, 6), guide = "prism_offset") + scale_y_continuous(limits = c(10, 35), guide = "prism_offset") + theme(axis.ticks.length = unit(10, "pt"), axis.ticks = element_line(colour = "red"), axis.line = element_line(colour = "blue"))
```

--------------------------------

### guide_prism_offset()

Source: https://context7.com/csdaw/ggprism/llms.txt

Axis guide that draws the axis line only between the outermost tick marks, creating an "offset axis" style from GraphPad Prism.

```APIDOC
## guide_prism_offset()

Axis guide that draws the axis line only between the outermost tick marks — a characteristic "offset axis" style from GraphPad Prism. Control the axis extent by adjusting `breaks` in the scale.

### Usage

Apply this guide to an axis scale using the `guide` argument in `scale_x_continuous()` or `scale_y_continuous()`, or via `guides()`.

### Parameters

- `breaks` (numeric vector, optional) - Defines the locations of the major tick marks, which also define the extent of the axis line.

### Examples

```r
library(ggplot2)
library(ggprism)

base <- ggplot(mtcars, aes(x = wt, y = mpg)) +
  geom_point() +
  theme(axis.line = element_line(colour = "black"))

# Apply offset guide to both axes
base +
  scale_x_continuous(limits = c(1, 6), breaks = seq(1, 6, by = 1), guide = "prism_offset") +
  scale_y_continuous(guide = "prism_offset")
```
```

--------------------------------

### Create Offset Axis with guide_prism_offset

Source: https://context7.com/csdaw/ggprism/llms.txt

guide_prism_offset creates an axis guide that draws the axis line only between the outermost tick marks, characteristic of GraphPad Prism's offset axis style. Adjust 'breaks' in the scale to control the axis extent.

```r
library(ggplot2)
library(ggprism)

base <- ggplot(mtcars, aes(x = wt, y = mpg)) +
  geom_point() +
  theme(axis.line = element_line(colour = "black"))

# Apply offset guide to both axes
base +
  scale_x_continuous(
    limits = c(1, 6),
    breaks = seq(1, 6, by = 1),
    guide  = "prism_offset"
  ) +
  scale_y_continuous(guide = "prism_offset")
```

--------------------------------

### Basic ggplot2 setup with ggprism customization

Source: https://github.com/csdaw/ggprism/blob/master/README.md

This code demonstrates setting up a ggplot object with ToothGrowth data and then applying ggprism themes, color scales, fill scales, and p-value annotations. It requires loading both ggplot2 and ggprism libraries.

```r
library(ggplot2)
library(ggprism)

tg <- ToothGrowth
tg$dose <- as.factor(tg$dose)

base <- ggplot(tg, aes(x = dose, y = len)) + 
  geom_violin(aes(colour = dose, fill = dose), trim = FALSE) + 
  geom_boxplot(aes(fill = dose), width = 0.2, colour = "black") + 
  scale_y_continuous(limits = c(-5, 40))

p_vals <- tibble::tribble(
  ~group1, ~group2, ~p.adj,   ~y.position,
  "0.5",   "1",     8.80e-14, 35,
  "0.5",   "2",     1.27e-7,  39
)
```

```r
base

base + 
  scale_color_prism("floral") + 
  scale_fill_prism("floral") + 
  guides(y = "prism_offset_minor") + 
  theme_prism(base_size = 16) + 
  theme(legend.position = "none") + 
  add_pvalue(p_vals, label = "p = {p.adj}", tip.length = 0, label.size = 4)
```

--------------------------------

### Install ggprism from CRAN

Source: https://github.com/csdaw/ggprism/blob/master/README.md

Use this command to install the latest stable version of the ggprism package from the Comprehensive R Archive Network (CRAN).

```r
install.packages("ggprism")
```

--------------------------------

### guide_prism_minor()

Source: https://context7.com/csdaw/ggprism/llms.txt

Axis guide that adds minor tick marks between major ticks, mimicking GraphPad Prism's style. Minor tick length is controlled by `prism.ticks.length` theme element.

```APIDOC
## guide_prism_minor()

Axis guide that adds minor tick marks between the standard major ticks, mirroring the minor-tick style common in GraphPad Prism. Minor tick length is controlled via the custom `prism.ticks.length` theme element.

### Usage

Apply this guide to an axis scale using the `guide` argument in `scale_x_continuous()` or `scale_y_continuous()`, or via `guides()`.

### Parameters

- `minor_breaks` (numeric vector, optional) - Specifies the locations of the minor tick marks.

### Examples

```r
library(ggplot2)
library(ggprism)

base <- ggplot(mtcars, aes(x = wt, y = mpg)) + geom_point()

# Add minor ticks to both axes
base + scale_x_continuous(guide = "prism_minor") + scale_y_continuous(guide = "prism_minor")

# Control number of minor ticks via minor_breaks
base + scale_x_continuous(minor_breaks = seq(0, 6, 0.5), guide = "prism_minor") + scale_y_continuous(minor_breaks = seq(10, 35, 1.25), guide = "prism_minor")

# Log10 axis with minor ticks
ggplot(msleep, aes(bodywt, brainwt)) + geom_point(na.rm = TRUE) +
  scale_x_log10(minor_breaks = rep(1:9, 4) * (10^rep(0:3, each = 9)), guide = "prism_minor")
```
```

--------------------------------

### Add Minor Ticks with guide_prism_minor

Source: https://context7.com/csdaw/ggprism/llms.txt

Use guide_prism_minor for an axis guide that adds minor tick marks between major ticks, mimicking GraphPad Prism's style. Minor tick length is controlled by the 'prism.ticks.length' theme element. Minor breaks can be specified.

```r
library(ggplot2)
library(ggprism)

base <- ggplot(mtcars, aes(x = wt, y = mpg)) + geom_point()

# Add minor ticks to both axes
base +
  scale_x_continuous(limits = c(0, 6), guide = "prism_minor") +
  scale_y_continuous(limits = c(10, 35), guide = "prism_minor")

# Use guides() shorthand
base + guides(x = "prism_minor", y = "prism_minor")

# Control number of minor ticks via minor_breaks
base +
  scale_x_continuous(
    limits       = c(0, 6),
    minor_breaks = seq(0, 6, 0.5),
    guide        = "prism_minor"
  ) +
  scale_y_continuous(
    limits       = c(10, 35),
    minor_breaks = seq(10, 35, 1.25),
    guide        = "prism_minor"
  ) +
  theme(
    axis.ticks.length  = unit(10, "pt"),  # major tick length
    prism.ticks.length = unit(5, "pt")    # minor tick length
  )

# Log10 axis with minor ticks at each mantissa
ggplot(msleep, aes(bodywt, brainwt)) +
  geom_point(na.rm = TRUE) +
  scale_x_log10(
    limits       = c(1e0, 1e4),
    minor_breaks = rep(1:9, 4) * (10^rep(0:3, each = 9)),
    guide        = "prism_minor"
  )
```

--------------------------------

### prism_fill_pal()

Source: https://context7.com/csdaw/ggprism/llms.txt

Low-level function to get a fill colour-generating function for a named Prism palette. Returns a function that produces hex fill colours.

```APIDOC
## prism_fill_pal()

Low-level fill palette function — the fill counterpart to `prism_colour_pal()`. Returns a function that produces hex fill colours.

### Parameters

- `palette` (character) - The name of the fill palette. See `ggprism_data$fill_palettes` for available options.
- `alpha` (numeric, optional) - Alpha transparency for the colours.

### Returns

A function that takes an integer `n` and returns `n` fill colours from the specified palette.

### Examples

```r
library(ggprism)

# Retrieve 3 fill colours from "flames"
prism_fill_pal(palette = "flames")(3)

# Inspect maximum capacity
pal <- prism_fill_pal("ocean")
attr(pal, "max_n")
```
```

--------------------------------

### prism_colour_pal() / prism_color_pal()

Source: https://context7.com/csdaw/ggprism/llms.txt

Low-level function to get a colour-generating function for a named Prism palette. Useful for retrieving raw hex colour codes.

```APIDOC
## prism_colour_pal() / prism_color_pal()

Low-level palette function that returns a colour-generating function for a named Prism palette. Useful when you need the raw hex colour codes outside of a scale context.

### Parameters

- `palette` (character) - The name of the colour palette. See `ggprism_data$colour_palettes` for available options.
- `alpha` (numeric, optional) - Alpha transparency for the colours.

### Returns

A function that takes an integer `n` and returns `n` colours from the specified palette.

### Examples

```r
library(ggprism)
library(scales)

# Get the first 4 colours from the "starry" palette
prism_colour_pal(palette = "starry")(4)

# Show all colours in a palette visually
show_palette <- function(palette) {
  pal_fn  <- prism_colour_pal(palette = palette)
  n_max   <- attr(pal_fn, "max_n")
  scales::show_col(pal_fn(n_max))
}
show_palette("pearl")
```
```

--------------------------------

### prism_shape_pal()

Source: https://context7.com/csdaw/ggprism/llms.txt

Low-level function to get a shape palette function. Returns a function that produces R `pch` integer codes for Prism-style point symbols.

```APIDOC
## prism_shape_pal()

Low-level shape palette function. Returns a function that produces R `pch` integer codes corresponding to Prism-style point symbols.

### Parameters

- `palette` (character) - The name of the shape palette. Options: `"default"`, `"filled"`, `"complete"`.

### Returns

A function that takes an integer `n` and returns `n` `pch` codes from the specified palette.

### Examples

```r
library(ggprism)
library(ggplot2)

# Retrieve 3 pch codes from the "filled" palette
prism_shape_pal(palette = "filled")(3)

# Use directly in geom_point
ggplot(mtcars, aes(x = wt, y = mpg)) + geom_point(shape = prism_shape_pal("default")(1), size = 4)
```
```

--------------------------------

### Get Prism Fill Palettes

Source: https://context7.com/csdaw/ggprism/llms.txt

prism_fill_pal is the fill counterpart to prism_colour_pal, returning a function that produces hex fill colors. The 'max_n' attribute indicates the maximum number of colors available in the palette.

```r
library(ggprism)

# All fill palettes and their sizes
lengths(ggprism_data$fill_palettes)

# Retrieve 3 fill colours from "flames"
prism_fill_pal(palette = "flames")(3)
#> [1] "#B61F26" "#E36B23" "#F9A03F"

# Inspect maximum capacity
pal <- prism_fill_pal("ocean")
attr(pal, "max_n")
```

--------------------------------

### Get Prism Shape Palettes

Source: https://context7.com/csdaw/ggprism/llms.txt

prism_shape_pal returns a function that produces R pch integer codes for Prism-style point symbols. The 'max_n' attribute indicates the maximum number of shapes available in the palette.

```r
library(ggprism)

# Retrieve 3 pch codes from the "filled" palette
prism_shape_pal(palette = "filled")(3)
#> [1] 19 15 17

# Maximum number of shapes
pal <- prism_shape_pal("complete")
attr(pal, "max_n")  # 14

# Use directly in geom_point
library(ggplot2)
ggplot(mtcars, aes(x = wt, y = mpg)) +
  geom_point(shape = prism_shape_pal("default")(1), size = 4)
```

--------------------------------

### Get Prism Color Palettes

Source: https://context7.com/csdaw/ggprism/llms.txt

prism_colour_pal returns a color-generating function for a named Prism palette. Useful for obtaining raw hex color codes outside of a scale context. The 'max_n' attribute indicates the palette's capacity.

```r
library(ggprism)
library(scales)

# List all palettes with their sizes
lengths(ggprism_data$colour_palettes)

# Get the first 4 colours from the "starry" palette
prism_colour_pal(palette = "starry")(4)
#> [1] "#2D2B55" "#5C5CA0" "#9DA7D5" "#C4C9E8"

# Show all colours in a palette visually
show_palette <- function(palette) {
  pal_fn  <- prism_colour_pal(palette = palette)
  n_max   <- attr(pal_fn, "max_n")
  scales::show_col(pal_fn(n_max))
}
show_palette("pearl")
show_palette("candy_bright")

# Use max_n attribute to know the palette's capacity
pal <- prism_colour_pal("floral")
attr(pal, "max_n")  # e.g. 9
```

--------------------------------

### scale_fill_prism()

Source: https://context7.com/csdaw/ggprism/llms.txt

Discrete fill scale using GraphPad Prism palettes. Direct counterpart to `scale_colour_prism()` for `fill` aesthetics.

```APIDOC
## scale_fill_prism()

### Description
Discrete fill scale using GraphPad Prism palettes. Direct counterpart to `scale_colour_prism()` for `fill` aesthetics.

### Usage
```r
library(ggplot2)
library(ggprism)

# List all available fill palettes
lengths(ggprism_data$fill_palettes)

tg <- ToothGrowth
tg$dose <- as.factor(tg$dose)

ggplot(tg, aes(x = dose, y = len, fill = dose)) +
  geom_boxplot() +
  scale_fill_prism(palette = "colorblind_safe") +
  theme_prism()

# Use "warm_and_sunny" palette with custom legend
ggplot(mpg, aes(x = class, y = hwy, fill = class)) +
  geom_violin() +
  scale_fill_prism(
    palette = "warm_and_sunny",
    name    = "Car class",
    labels  = function(x) tools::toTitleCase(x)
  ) +
  theme_prism(axis_text_angle = 45)
```
```

--------------------------------

### preview_theme()

Source: https://context7.com/csdaw/ggprism/llms.txt

Quickly preview any named ggprism theme palette as a boxplot using a generated colour-spread dataset — useful for choosing a palette before applying it.

```APIDOC
## preview_theme()

### Description
Quickly preview any named ggprism theme palette as a boxplot using a generated colour-spread dataset — useful for choosing a palette before applying it.

### Usage
```r
library(ggplot2)
library(ggprism)

# See all available theme names
names(ggprism_data$themes)
#> [1] "all_null"      "black_and_white" "blueprint"  "candy_bright"
#> [5] "candy_soft"    "colorblind_safe" "earth_tones" "floral" ...

# Preview a specific theme — returns a ggplot object
preview_theme("floral")
preview_theme("candy_bright")
preview_theme("office")
```
```

--------------------------------

### Apply GraphPad Prism Theme

Source: https://context7.com/csdaw/ggprism/llms.txt

Use theme_prism() to apply a GraphPad Prism-style theme. It supports various palettes and customization options like font, size, and borders. Ensure coord_cartesian(clip = "off") is used when border = TRUE.

```r
library(ggplot2)
library(ggprism)

# List all available theme palettes
names(ggprism_data$themes)

# Basic usage: default "black_and_white" palette
ggplot(mpg, aes(x = displ, y = cty, colour = class)) +
  geom_point() +
  theme_prism()

# Use a different theme palette and match the colour scale
ggplot(mpg, aes(x = displ, y = cty, colour = class)) +
  geom_point() +
  theme_prism(palette = "stained_glass") +
  scale_color_prism(palette = "stained_glass")

# Rotate x-axis text, change font, and add a border
ggplot(mpg, aes(x = class, y = hwy, fill = class)) +
  geom_boxplot() +
  theme_prism(
    palette       = "floral",
    base_size     = 16,
    base_family   = "serif",
    base_fontface = "plain",
    axis_text_angle = 45,
    border        = TRUE
  ) +
  scale_fill_prism(palette = "floral") +
  coord_cartesian(clip = "off")  # required when border = TRUE

# Change border thickness separately from base_size
ggplot(mtcars, aes(x = wt, y = mpg)) +
  geom_point() +
  theme_prism(border = TRUE, base_size = 14, base_rect_size = 2) +
  coord_cartesian(clip = "off")
```

--------------------------------

### scale_colour_prism() / scale_color_prism()

Source: https://context7.com/csdaw/ggprism/llms.txt

Discrete colour scale using one of GraphPad Prism's named colour palettes. Works identically to `scale_colour_manual()` but pulls from the built-in ggprism palette library.

```APIDOC
## scale_colour_prism() / scale_color_prism()

### Description
Discrete colour scale using one of GraphPad Prism's named colour palettes. Works identically to `scale_colour_manual()` but pulls from the built-in ggprism palette library.

### Usage
```r
library(ggplot2)
library(ggprism)

# List all palettes and their maximum number of colours
lengths(ggprism_data$colour_palettes)

base <- ggplot(mtcars, aes(x = wt, y = mpg, colour = factor(cyl))) +
  geom_point(size = 3)

# Apply a palette
base + scale_colour_prism(palette = "candy_bright")

# With custom legend title and labels
base +
  scale_colour_prism(
    palette = "candy_bright",
    name    = "Cylinders",
    labels  = c("4 cyl", "6 cyl", "8 cyl")
  )

# Change legend label order
base +
  scale_colour_prism(
    palette = "candy_bright",
    name    = "Cylinders",
    breaks  = c(8, 4, 6)
  )

# Combine colour and fill scales
ggplot(mpg, aes(x = class, y = hwy, fill = class, colour = class)) +
  geom_boxplot() +
  scale_fill_prism(palette = "floral") +
  scale_colour_prism(palette = "floral")
```
```

--------------------------------

### Offset Axis with Minor Ticks (guide_prism_offset_minor)

Source: https://context7.com/csdaw/ggprism/llms.txt

Applies the guide_prism_offset_minor to continuous axes, combining offset axis lines with minor tick marks. This is useful for detailed axis representation on continuous scales.

```r
base + scale_x_continuous(limits = c(0, 6), minor_breaks = seq(0, 6, 0.5), guide = "prism_offset_minor") + scale_y_continuous(limits = c(10, 35), minor_breaks = seq(10, 35, 1.25), guide = "prism_offset_minor") + theme(axis.ticks.length = unit(10, "pt"), prism.ticks.length = unit(5, "pt"))
```

```r
ggplot(msleep, aes(bodywt, brainwt)) + geom_point(na.rm = TRUE) + scale_x_log10(limits = c(1e0, 1e4), minor_breaks = rep(1:9, 4) * (10^rep(0:3, each = 9)), guide = "prism_offset_minor") + theme(axis.line = element_line(colour = "black"))
```

--------------------------------

### theme_prism()

Source: https://context7.com/csdaw/ggprism/llms.txt

Apply a GraphPad Prism-style ggplot2 theme with bold fonts, no gridlines, clean axes, and optional coloured backgrounds drawn from named Prism colour schemes.

```APIDOC
## theme_prism()

### Description
Apply a GraphPad Prism-style ggplot2 theme with bold fonts, no gridlines, clean axes, and optional coloured backgrounds drawn from named Prism colour schemes.

### Usage
```r
library(ggplot2)
library(ggprism)

# List all available theme palettes
names(ggprism_data$themes)

# Basic usage: default "black_and_white" palette
ggplot(mpg, aes(x = displ, y = cty, colour = class)) +
  geom_point() +
  theme_prism()

# Use a different theme palette and match the colour scale
ggplot(mpg, aes(x = displ, y = cty, colour = class)) +
  geom_point() +
  theme_prism(palette = "stained_glass") +
  scale_color_prism(palette = "stained_glass")

# Rotate x-axis text, change font, and add a border
ggplot(mpg, aes(x = class, y = hwy, fill = class)) +
  geom_boxplot() +
  theme_prism(
    palette       = "floral",
    base_size     = 16,
    base_family   = "serif",
    base_fontface = "plain",
    axis_text_angle = 45,
    border        = TRUE
  ) +
  scale_fill_prism(palette = "floral") +
  coord_cartesian(clip = "off")  # required when border = TRUE

# Change border thickness separately from base_size
ggplot(mtcars, aes(x = wt, y = mpg)) +
  geom_point() +
  theme_prism(border = TRUE, base_size = 14, base_rect_size = 2) +
  coord_cartesian(clip = "off")
```
```

--------------------------------

### Preview ggprism Theme Palettes

Source: https://context7.com/csdaw/ggprism/llms.txt

Use preview_theme() to quickly visualize any named ggprism theme palette. This function generates a boxplot using a sample dataset, aiding in palette selection before application.

```r
library(ggplot2)
library(ggprism)

# See all available theme names
names(ggprism_data$themes)
#> [1] "all_null"      "black_and_white" "blueprint"  "candy_bright"
#> [5] "candy_soft"    "colorblind_safe" "earth_tones" "floral" ...

# Preview a specific theme — returns a ggplot object
preview_theme("floral")
preview_theme("candy_bright")
preview_theme("office")
```

--------------------------------

### Apply Prism Discrete Colour Scale

Source: https://context7.com/csdaw/ggprism/llms.txt

Use scale_colour_prism() or scale_color_prism() for discrete colour scales with GraphPad Prism palettes. It functions like scale_colour_manual() but uses built-in ggprism palettes. Custom legend titles, labels, and order are supported.

```r
library(ggplot2)
library(ggprism)

# List all palettes and their maximum number of colours
lengths(ggprism_data$colour_palettes)

base <- ggplot(mtcars, aes(x = wt, y = mpg, colour = factor(cyl))) +
  geom_point(size = 3)

# Apply a palette
base + scale_colour_prism(palette = "candy_bright")

# With custom legend title and labels
base +
  scale_colour_prism(
    palette = "candy_bright",
    name    = "Cylinders",
    labels  = c("4 cyl", "6 cyl", "8 cyl")
  )

# Change legend label order
base +
  scale_colour_prism(
    palette = "candy_bright",
    name    = "Cylinders",
    breaks  = c(8, 4, 6)
  )

# Combine colour and fill scales
ggplot(mpg, aes(x = class, y = hwy, fill = class, colour = class)) +
  geom_boxplot() +
  scale_fill_prism(palette = "floral") +
  scale_colour_prism(palette = "floral")
```

--------------------------------

### Apply Prism Discrete Fill Scale

Source: https://context7.com/csdaw/ggprism/llms.txt

Use scale_fill_prism() for discrete fill scales, mirroring scale_colour_prism() for the fill aesthetic. It allows selection from GraphPad Prism palettes and customization of legend titles and labels.

```r
library(ggplot2)
library(ggprism)

# List all available fill palettes
lengths(ggprism_data$fill_palettes)

tg <- ToothGrowth
tg$dose <- as.factor(tg$dose)

ggplot(tg, aes(x = dose, y = len, fill = dose)) +
  geom_boxplot() +
  scale_fill_prism(palette = "colorblind_safe") +
  theme_prism()

# Use "warm_and_sunny" palette with custom legend
ggplot(mpg, aes(x = class, y = hwy, fill = class)) +
  geom_violin() +
  scale_fill_prism(
    palette = "warm_and_sunny",
    name    = "Car class",
    labels  = function(x) tools::toTitleCase(x)
  ) +
  theme_prism(axis_text_angle = 45)
```

--------------------------------

### Scale Shapes with Prism Palettes

Source: https://context7.com/csdaw/ggprism/llms.txt

Use scale_shape_prism to map factor levels to GraphPad Prism-style point symbols. Offers 'default', 'filled', and 'complete' palettes. Custom legend titles and labels can be applied.

```r
library(ggplot2)
library(ggprism)

# Inspect available shape palettes
ggprism_data$shape_palettes

base <- ggplot(mtcars, aes(x = wt, y = mpg, shape = factor(cyl))) +
  geom_point(size = 4)

# Default palette (9 shapes, no fill)
base + scale_shape_prism(palette = "default")

# Filled palette (first 5 shapes have fill)
base + scale_shape_prism(palette = "filled")

# Complete palette (14 shapes)
base + scale_shape_prism(palette = "complete")

# Custom legend title and labels
base +
  scale_shape_prism(
    palette = "filled",
    name    = "Cylinders",
    labels  = c("4-cyl", "6-cyl", "8-cyl")
  )

# Visualise all shapes in a palette
show_shapes <- function(palette) {
  df <- ggprism_data$shape_palettes[[palette]][, -1]
  df$pch_f <- factor(df$pch, levels = df$pch)
  ggplot(df, aes(x = 0, y = 0, shape = pch)) +
    geom_point(aes(shape = pch), size = 5, fill = "red") +
    scale_shape_identity() +
    facet_wrap (~ pch_f) +
    theme_void()
}
show_shapes("complete")
```

--------------------------------

### Annotation Ticks for Mirrored and Minor Ticks

Source: https://context7.com/csdaw/ggprism/llms.txt

Shows how to use annotation_ticks to add tick marks as an annotation layer, useful for mirrored ticks on bordered plots or minor ticks on secondary axes. Customization of tick appearance is also demonstrated.

```r
ggplot(mtcars, aes(x = mpg, y = disp)) + geom_point() + theme_prism(border = TRUE) + coord_cartesian(clip = "off") + annotation_ticks(sides = "tr", type = "major", outside = TRUE) + theme(plot.margin = unit(c(4, 4, 4, 4), "mm"))
```

```r
ggplot(mtcars, aes(x = mpg, y = disp)) + geom_point() + scale_x_continuous(guide = "prism_minor") + scale_y_continuous(guide = "prism_minor") + theme_prism(border = TRUE) + coord_cartesian(clip = "off") + annotation_ticks(sides = "tr", type = "both", outside = TRUE) + theme(plot.margin = unit(c(4, 4, 4, 4), "mm"))
```

```r
ggplot(sample_data, aes(x = day)) + geom_line(aes(y = temperature), colour = "magenta") + geom_line(aes(y = price / 10), colour = "blue") + scale_y_continuous(sec.axis = sec_axis(~. * 10, name = "price"), guide = "prism_minor") + theme_prism(border = TRUE) + coord_cartesian(clip = "off") + annotation_ticks(sides = "r", type = "minor", outside = TRUE)
```

```r
ggplot(mtcars, aes(x = mpg, y = disp)) + geom_point() + theme_prism(border = TRUE) + coord_cartesian(clip = "off") + annotation_ticks(sides = "tr", type = "major", outside = TRUE, tick.length = unit(10, "pt"), colour = "red", linewidth = 2, linetype = "dashed")
```

--------------------------------

### scale_shape_prism()

Source: https://context7.com/csdaw/ggprism/llms.txt

Applies GraphPad Prism-style point symbols to shapes in ggplot2 plots. Supports different palettes and custom legend options.

```APIDOC
## scale_shape_prism()

Discrete shape scale that maps factor levels to GraphPad Prism-style point symbols. Offers three palettes: `"default"` (9 unfilled symbols), `"filled"` (10 symbols, first 5 filled), and `"complete"` (14 symbols).

### Parameters

- `palette` (character) - The name of the shape palette to use. Options: `"default"`, `"filled"`, `"complete"`.
- `name` (character, optional) - The title for the legend.
- `labels` (character vector, optional) - Custom labels for the legend.

### Examples

```r
library(ggplot2)
library(ggprism)

base <- ggplot(mtcars, aes(x = wt, y = mpg, shape = factor(cyl))) + geom_point(size = 4)

# Default palette
base + scale_shape_prism(palette = "default")

# Filled palette
base + scale_shape_prism(palette = "filled")

# Complete palette
base + scale_shape_prism(palette = "complete")

# Custom legend title and labels
base + scale_shape_prism(palette = "filled", name = "Cylinders", labels = c("4-cyl", "6-cyl", "8-cyl"))
```
```

--------------------------------

### geom_bracket()

Source: https://context7.com/csdaw/ggprism/llms.txt

Low-level geom that draws a square bracket from (x, y) to (xend, yend). Used internally by add_pvalue() but can be used directly for custom bracket annotations.

```APIDOC
## geom_bracket()

Low-level geom that draws a square bracket from `(x, y)` to `(xend, yend)`. Used internally by `add_pvalue()` but can be used directly for custom bracket annotations.

### Minimal bracket
```r
library(ggplot2)
library(ggprism)

ggplot(
  data.frame(x = 1, xend = 4, y = 1, yend = 1),
  aes(x = x, xend = xend, y = y, yend = yend)
) +
  geom_bracket()
```

### Custom tip length and direction
```r
ggplot(
  data.frame(x = 1, xend = 3, y = 5, yend = 5),
  aes(x = x, xend = xend, y = y, yend = yend)
) +
  geom_bracket(
    tip.length = c(0.2, 0.05),
    direction  = "up",
    colour     = "steelblue",
    linewidth  = 1
  )
```
```

--------------------------------

### Draw custom brackets with geom_bracket()

Source: https://context7.com/csdaw/ggprism/llms.txt

Use geom_bracket() for direct control over drawing square brackets between specified coordinates. Customize tip lengths, direction, color, and line width. This is a lower-level function used internally by add_pvalue().

```r
library(ggplot2)
library(ggprism)

# Minimal bracket
ggplot(
  data.frame(x = 1, xend = 4, y = 1, yend = 1),
  aes(x = x, xend = xend, y = y, yend = yend)
) +
  geom_bracket()
```

```r
# Custom tip length and direction
ggplot(
  data.frame(x = 1, xend = 3, y = 5, yend = 5),
  aes(x = x, xend = xend, y = y, yend = yend)
) +
  geom_bracket(
    tip.length = c(0.2, 0.05),
    direction  = "up",
    colour     = "steelblue",
    linewidth  = 1
  )
```

--------------------------------

### ggprism_data

Source: https://context7.com/csdaw/ggprism/llms.txt

Built-in list object providing the raw colour hex codes, fill hex codes, shape pch integers, and theme element colours used across all ggprism functions.

```APIDOC
## ggprism_data

Built-in list object providing the raw colour hex codes, fill hex codes, shape `pch` integers, and theme element colours used across all ggprism functions.

### Explore the structure
```r
library(ggprism)

# Explore the structure
str(ggprism_data, max.level = 1)
#> List of 4
#>  $ themes           :List of N  (named theme element colour tibbles)
#>  $ colour_palettes  :List of N  (named character vectors of hex codes)
#>  $ fill_palettes    :List of N  (named character vectors of hex codes)
#>  $ shape_palettes   :List of 3  (data frames with pch codes)
```

### List all theme names
```r
names(ggprism_data$themes)
```

### List all colour palettes and their sizes
```r
lengths(ggprism_data$colour_palettes)
```

### Get hex codes for the "ocean" colour palette
```r
ggprism_data$colour_palettes[["ocean"]]
```

### Get the default shape palette as a data frame
```r
ggprism_data$shape_palettes[["default"]]
```

### Access raw theme colours for "flames"
```r
ggprism_data$themes[["flames"]]
```
```

--------------------------------

### add_pvalue()

Source: https://context7.com/csdaw/ggprism/llms.txt

Adds p-value brackets (or text-only labels) to a ggplot from a data frame of statistical results. Supports glue-style label expressions, grouped/faceted plots, dodged data, customisable bracket aesthetics, and plotmath expressions.

```APIDOC
## add_pvalue()

Adds p-value brackets (or text-only labels) to a ggplot from a data frame of statistical results. Supports glue-style label expressions, grouped/faceted plots, dodged data, customisable bracket aesthetics, and plotmath expressions.

### Basic bracket comparing two groups
```r
library(ggplot2)
library(ggprism)

tg      <- ToothGrowth
tg$dose <- as.factor(tg$dose)

two_means <- tibble::tribble(
  ~group1, ~group2, ~p,     ~y.position,
  "OJ",    "VC",    0.0606, 36
)

ggplot(tg, aes(x = supp, y = len)) +
  geom_boxplot() +
  add_pvalue(two_means)
```

### Glue expression label with plotmath parsing
```r
ggplot(tg, aes(x = supp, y = len)) +
  geom_boxplot() +
  add_pvalue(two_means, label = "p = {p}", parse = TRUE)
```

### Custom bracket and label aesthetics
```r
ggplot(tg, aes(x = supp, y = len)) +
  geom_boxplot() +
  add_pvalue(
    two_means,
    label           = "p = {p}",
    parse           = TRUE,
    colour          = "red",
    label.size      = 5,
    fontface        = "bold",
    bracket.colour  = "blue",
    bracket.size    = 1.2,
    tip.length      = c(0.1, 0),   # asymmetric tips
    linetype        = "dashed"
  )
```

### Pairwise comparisons with bracket shortening
```r
pairwise <- tibble::tribble(
  ~group1, ~group2, ~p.signif, ~y.position,
  "0.5",   "1",     "****",    38,
  "0.5",   "2",     "****",    36,
  "1",     "2",     "****",    38
)

ggplot(tg, aes(x = dose, y = len)) +
  geom_boxplot(aes(fill = dose)) +
  add_pvalue(pairwise, bracket.shorten = c(0.05, 0, 0.05)) +
  scale_fill_prism(palette = "floral") +
  theme_prism()
```

### Grouped data: step spacing between brackets
```r
pairwise_grouped <- tibble::tribble(
  ~group1, ~group2, ~p.adj,  ~y.position, ~supp,
  "0.5",   "1",     2.63e-4, 33.5,        "OJ",
  "0.5",   "2",     3.96e-6, 37.6,        "OJ",
  "1",     "2",     1.18e-1, 41.6,        "OJ",
  "0.5",   "1",     2.04e-6, 36.5,        "VC",
  "0.5",   "2",     1.40e-7, 40.6,        "VC",
  "1",     "2",     2.75e-4, 44.6,        "VC"
)

ggplot(tg, aes(x = dose, y = len)) +
  geom_boxplot(aes(fill = supp)) +
  add_pvalue(
    pairwise_grouped,
    colour        = "supp",
    tip.length    = 0,
    step.group.by = "supp",
    step.increase = 0.03
  )
```

### Faceted plot: one bracket per facet
```r
facet_stats <- tibble::tribble(
  ~group1, ~group2, ~p.adj,  ~y.position, ~dose,
  "OJ",    "VC",    0.0127,  24,          "0.5",
  "OJ",    "VC",    0.00312, 30,          "1",
  "OJ",    "VC",    0.964,   36.5,        "2"
)

ggplot(tg, aes(x = supp, y = len)) +
  geom_boxplot() +
  facet_wrap(~ dose, scales = "free") +
  add_pvalue(facet_stats)  # data frame must contain the faceting column
```

### Text-only label (no bracket)
```r
ggplot(tg, aes(x = supp, y = len)) +
  geom_boxplot() +
  add_pvalue(two_means, remove.bracket = TRUE, x = 1.5)
```

### Non-default column names
```r
custom_cols <- tibble::tribble(
  ~left,  ~right, ~significance, ~height,
  "OJ",   "VC",   "ns",          36
)

ggplot(tg, aes(x = supp, y = len)) +
  geom_boxplot() +
  add_pvalue(
    custom_cols,
    xmin       = "left",
    xmax       = "right",
    label      = "significance",
    y.position = "height"
  )
```
```

--------------------------------

### Access ggprism built-in data

Source: https://context7.com/csdaw/ggprism/llms.txt

ggprism_data is a list containing raw color hex codes, fill hex codes, shape pch integers, and theme element colors used in ggprism. Explore its structure and access specific palettes or theme colors.

```r
library(ggprism)

# Explore the structure
str(ggprism_data, max.level = 1)
#> List of 4
#>  $ themes           :List of N  (named theme element colour tibbles)
#>  $ colour_palettes  :List of N  (named character vectors of hex codes)
#>  $ fill_palettes    :List of N  (named character vectors of hex codes)
#>  $ shape_palettes   :List of 3  (data frames with pch codes)
```

```r
# List all theme names
names(ggprism_data$themes)
```

```r
# List all colour palettes and their sizes
lengths(ggprism_data$colour_palettes)
```

```r
# Get hex codes for the "ocean" colour palette
ggprism_data$colour_palettes[["ocean"]]
```

```r
# Get the default shape palette as a data frame
ggprism_data$shape_palettes[["default"]]
```

```r
# Access raw theme colours for "flames"
ggprism_data$themes[["flames"]]
```