--- 
title: "Getting Started with `ggpackets`" 
author: "Doug Kelkhoff" 
date: "`r Sys.time()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Getting Started with `ggpackets`}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include=FALSE} 
knitr::opts_chunk$set(
  echo = TRUE, 
  fig.align='center', 
  fig.width = 6,
  fig.height = 4,
  out.width = '600px', 
  out.height = '400px') 
library(ggpackets)
```

# Overview

`ggpackets` aims to make ggplot plots more modular by adding a framework for 
packing groups of ggplot layers that can be stored as a single variable or 
accessed from a function call. This means that you can now easily build out 
template plots which still interact nicely with the ggplot syntax. To illustrate
this functionality, let's start with a trivial example.


## First, our trusted ggplot

To start, let's take a look at what it might take to build a bar plot showing 
the mean value of some group with some errorbars to represent standard deviation
and the counts in each bar labelled at the base of the bar. We'll start by
building this plot using standard `ggplot`.

```{r libraries, message = FALSE, warning = FALSE}
library(ggplot2)
```

```{r ex1.ggplot, warning = FALSE} 
ggplot(mtcars) + 
  aes(x = carb, y = mpg) + 
  geom_bar(stat= 'summary', aes(y = mpg), 
    fun.data = function(c) c(y = mean(c))) + 
  geom_errorbar(stat = 'summary', aes(y = mpg), width = 0.2,
    fun.y = mean,
    fun.min = ~mean(.) - sd(.),
    fun.max = ~mean(.) + sd(.)) + 
  geom_text(stat = 'summary', vjust = -0.5, color = 'white',
    fun.data = function(c) c(
      label = length(c), 
      y = 0))
```

Wow! that plot got out of hand fast. And you can see that there's a lot of 
repeated code. If we know that we want to use the exact same code repeatedly, we
could wrap this in a function and make it a bit more reusable, but we'd 
sacrifice a lot of the customizability of building our plot from scratch for 
minor modifications in each instance. Alternatively, we could use `ggpackets`,
which would provide further functionality to interoperate with other ggplot
layers.

# Packing Some Layers

In its most straightforward form, `ggpackets` allows for the packing of multiple
layers together into a single variable. This variable contains a `ggppacket` 
object. This class handles addition with other `ggpacket` objects and `ggproto` 
objects to append them or their contents to an internal list of `ggproto` layers
( `ggproto` objects are the result of any of the `geom_*` or `stat_*` functions in 
`ggplot2`). When it's combined with a ggplot call to build a plot (starting with
the function `ggplot()`), the `ggpacket` will add its layers to the ggplot.

## Enter `ggpacket`

```{r ex1.ggpackets.ex0}
my_ggpk_layers <- ggpacket() + 
  geom_bar(stat = 'summary', 
    fun.data = function(c) c(y = mean(c))) + 
  geom_errorbar(stat = 'summary', width = 0.2,
    fun.data = function(c) c(
      y = mean(c),
      ymin = mean(c) - sd(c),
      ymax = mean(c) + sd(c))) +
  geom_text(stat = 'summary', vjust = -0.5,
    color = 'white',
    fun.data = function(c) c(label = length(c), y = 0))
```

```{r, warning = FALSE}
ggplot(mtcars) + 
  aes(x = carb, y = mpg, fill = as.factor(am)) + 
  my_ggpk_layers() + 
  facet_grid(. ~ am, scales = 'free')
```

By breaking out only the layers of the plot, we still retain full control over
the additional layers that might be needed and the variables that are being used
to produce the plot without needing to add extensive argument handling to a
function.

## Building Functions with `ggplot2`

Using `ggpacket()` to build out a packet of layers, we get a bunch of 
flexibility to provide modifications to our base ggplot layers with only a very 
minor change to our code. Let's say we instead want a bit more fine-grained 
control over the explicit behavior of our custom plot. This is where the most 
straightforward usage of `ggpackets` might not suffice and we might turn to a 
function to fullfil our needs. At this point, wrapping our original ggplot call
in a function starts to become pretty appealing.

```{r ex1.ggplot.func}
my_plot <- function(data, x, y, fun.data = mean_se) {
  ggplot(data) + 
    aes_string(x = x, y = y) +
    
    geom_bar(stat= 'summary', 
      aes_string(y = y), 
      fun.data = fun.data) + 
    
    geom_errorbar(
      stat = 'summary', 
      aes_string(y = y), 
      width = 0.2,
      fun.data = fun.data) +
    
    geom_text(
      stat = 'summary', 
      color = 'white',
      vjust = -0.5, 
      fun.data = function(c) c(label = length(c), y = 0))
}
```

```{r, warning = FALSE}
my_plot(mtcars, 'carb', 'wt')
```

Looking pretty good!

Let's consider, however, that you still want to have the flexibility to edit the
color of the bars throughout your analysis, or change the function used to 
determine your errorbars, or facet your plot for multiple groups. One way would 
be to include additional arguments in your new function and then pass that 
through to your plot. Every additional argument requires a fair bit of tweaking 
to this function and it's fairly easy to imagine the scope of the function 
growing quickly out of hand. Alternatively, you could wrap your ggplot layers in
a list and use those in a ggplot, but you'd be constrained to the parameters
initially defined in the list.

## Building Functions with `ggpackets`

`ggpackets` aims to reduce this inevitable issue by making it as simple as
possible to build out these types of reusable code snippets.

```{r ex1.ggpackets2}
my_ggpk <- function(...) {
  ggpacket(...) %+%

  geom_bar(.id = 'bar',
    fun.data = mean_se,
    position = position_dodge(width = 1.0),
    ...,
    stat= 'summary') %+%
    
  geom_errorbar(.id = 'errorbar',
    fun.data = mean_se,
    position = position_dodge(width = 1.0),
    width = 0.2,
    ...,
    stat = 'summary') %+%

  geom_label(.id = 'label',
    position = position_dodge(width = 1.0),
    vjust = -0.5, color = 'white',
    alpha = 0.3, label.size = NA,
    ...,
    stat = 'summary',
    fun.data = function(d) c(label = length(d), y = 0))
}
```

```{r, warning = FALSE}
ggplot(mtcars) + 
  aes(x = carb, y = mpg) + 
  my_ggpk(fun.data = mean_se, bar.mapping = aes(fill = carb))
```

> **Tip:**
> 
> Use `ggplot2`'s lesser-used `%+%` operator to compose `ggpacket`s in order 
> to handle duplicate arguments without throwing warnings. `ggpackets` will
> use the last-enterred argument to build the plot, allowing a comfortable 
> syntax to intuitively set a default value while allowing user-flexibility.
>
> ````r
> f <- function(...) {
>   ggpacket(...) %+%              # all ... used as default for all layers
>     geom_bar(fill = "red") %+%   # overwrites any fill from ...
>     geom_bar(fill = "red", ...)  # allows ... to now mask the default
> }
> ````
>

This format, with only a bit of extra syntax, exposes quite a lot of new
functionality. We can use additional geometries by adding them to our plot in
standard `ggplot` fashion, we can alter our aesthetics intuitively and we can
modify the internals of our packed layers easily. To see this in action, let's
take a look at what we can do with this new function:

## Gallery

### Composes well with `ggplot` elements

```{r ggpackets.ex2, warning = FALSE}
ggplot(mtcars) + 
  aes(x = carb, y = wt, fill = vs) + 
  my_ggpk() + 
  facet_grid(. ~ vs, scales = 'free')
```

### Multiple `ggpackets` can be used together

```{r ggpackets.ex3, warning = FALSE}
my_ggpk2 <- ggpacket() + 
  geom_ribbon(stat = 'summary', fun.data = mean_se, alpha = 0.2) + 
  geom_line(stat = 'summary', fun.data = mean_se, alpha = 0.3, size = 2)

ggplot(mtcars) + 
  aes(x = carb, y = wt) + 
  my_ggpk() + 
  my_ggpk2
```

### Composing with `ggplot` annotations and themes

```{r ggpackets.ex4}
ggplot(mtcars) + 
  aes(x = carb, y = wt, fill = carb) + 
  my_ggpk() + 
  ggtitle('A beautiful ggpackets plot!') + 
  theme_light()
```