---
title: "Using config to control ggpedigree plots"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Using config to control ggpedigree plots}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 7,
  fig.height = 5
)
```

```{r libraries, message=FALSE, warning=FALSE}
library(ggpedigree) # ggPedigree lives here
library(BGmisc) # helper utilities & example data
library(ggplot2) # ggplot2 for plotting
library(viridis) # viridis for color palettes
library(tidyverse) # for data wrangling
```

This vignette demonstrates how to use the `config` argument to control the behavior of pedigree plots in the `{ggpedigree}` package.

Every gg-based plotting function in `{ggpedigree}` accepts a `config` argument. A `config` is a named list. Each element corresponds to one plotting, layout, or aesthetic option. You pass the list to the plotting function and the plot is drawn using those values.

You do not need to supply every option. You only provide the options you want to change. Any options you do not specify will use the package defaults. You can see a full list of supported options and their defaults by reviewing the documentation for `getDefaultPlotConfig()`.

This vignette demonstrates how `config` is used in practice. An extended list of all available options is provided in the online documentation.

# Basic usage of `config` in `ggPedigree()`

We will use the `potter` pedigree dataset bundled in `{BGmisc}`.

```{r}
library(BGmisc)
data("potter")
```

A basic pedigree plot uses defaults:

```{r}
ggPedigree(
  potter,
  famID = "famID",
  personID = "personID",
  momID = "momID",
  dadID = "dadID"
)
```

## Sex coding: `code_male` and `code_female`

`ggPedigree()` (and other ggpedigree plots that use sex) need to know how sex is encoded in your data so they can assign the correct **shapes** (and optionally **colors**) for female, male, and unknown.

The `code_male` and `code_female` config options define which values in your sex column should be treated as male vs female. The defaults assume:

-   `code_female = 0`
-   `code_male = 1`

If your dataset uses different codes (for example `1/2` or `"M"/"F"`), override these in `config`.

``` r
# Example: sex coded as 1 = male, 2 = female
ggPedigree(
  ped,
  famID = "famID",
  personID = "personID",
  momID = "momID",
  dadID = "dadID",
  config = list(
    code_male = 1,
    code_female = 2,
    code_unknown = 3
  )
)

# Example: sex coded as "M" / "F"
ggPedigree(
  ped,
  famID = "famID",
  personID = "personID",
  momID = "momID",
  dadID = "dadID",
  config = list(
    code_male = "M",
    code_female = "F"
  )
)
```

Once the sex codes are interpreted correctly, the plot uses the corresponding shape settings (`sex_shape_female`, `sex_shape_male`, `sex_shape_unknown`) and, when enabled, sex-based coloring (`sex_color_include`, `sex_color_palette`).


# Advanced Examples

Additional examples are available in the online documentation to keep the package file size reasonable. These are provided as articles that demonstrate more complex pedigree plots. You can find these on the [ggpedigree website](https://r-computing-lab.github.io/ggpedigree/).