---
title: "ggplot2 theme for scientific publications"
author: "Zacharias Steinmetz"
date: "`r Sys.Date()`"
output:
  html_document:
    keep_md: yes
    fig_width: 8
    fig_height: 5
vignette: >
  %\VignetteIndexEntry{ggplot2 theme for scientific publications}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include=FALSE, echo=FALSE}
knitr::opts_chunk$set(
  echo = TRUE,
  warning = FALSE, 
  message = FALSE,
  comment = "# >"
)
```

## Packages

First, load **ggplot2** alongside **envalysis**.

```{r packages}
library(envalysis)
library(ggplot2)
```

## Default theme

The following code chunk plots the **ggplot2** `mtcars` sample data set with the
default **ggplot2** theme.

```{r default_theme, fig.align="center"}
data("mtcars")

p <- ggplot(mtcars) +
  geom_point(aes(x = wt, y = mpg, color = factor(gear))) +
  labs(
    title = "Fuel economy declines as weight increases",
    subtitle = "(1973-74)",
    caption = "Data from the 1974 Motor Trend US magazine.",
    x = "Weight (1000 lbs)",
    y = "Fuel economy (mpg)",
    colour = "Gears"
  ) +
  facet_wrap( ~ am, labeller = labeller(am = c("0" = "Automatic",
                                               "1" = "Manual")))
p
```

## `theme_publish()`

Adding `theme_publish()` applies the custom theme.

```{r theme_publish, fig.align="center"}
p + theme_publish()
```

`theme_publish()` allows for changing the base font face, font size, and
line widths. More arguments may be passed to **ggplot2**'s `theme_bw()`

```{r theme_arguments, fig.align="center"}
p + theme_publish(base_size = 16, base_family = "Times", base_linewidth = 0.7)
```