In InStreamFisheries/IFRthemes: Functions to apply custom IFR ggplot2 themes

# knitr::opts_chunk$set(
#   collapse = TRUE,
#   comment = "#>"
# )

library(IFRthemes)
library(ggplot2)
library(dplyr)

Introduction

All IFR plots should be produced in ggplot2 using a standard theme and consistent colour palette. The IFRthemes package allows the user to apply a custom IFR theme and two different colour palettes depending on the number of colours required.

Installation

You can install the package from GitHub using the remotes::install_github function. Using build_vignettes = TRUE allows you to access this vignette.

remotes::install_github("InStreamFisheries/IFRthemes",
                        build_vignettes = TRUE, 
                        force = TRUE)
library(IFRthemes)

Once the package is installed, you can access this vignette via the following command:

browseVignettes("IFRthemes")

Custom Theme

To use the IFR theme, simply add + theme_ifr() to a ggplot object.

ggplot(mtcars, aes(mpg, disp)) + 
  geom_point(size = 3) + 
  theme_ifr()

The theme also formats panels.

ggplot(mtcars, aes(mpg, disp)) + 
  geom_point(size = 3) + 
  facet_wrap(~cyl) +
  theme_ifr()

Changing Plot Text Size

There is one argument to the theme: base_size, which scales the size of plot text. The function defaults to 16, which sizes nicely for 6 inch figures. In some cases (e.g., very large plots with lots of faceting) you may need to change the text size. The example below shows how to apply this argument.

ggplot(mtcars, aes(mpg, disp)) + 
  geom_point(size = 3) + 
  facet_wrap(~cyl) +
  theme_ifr(base_size = 10)

Overwriting the Theme

It's easy to adjust the theme. Below the theme is overwritten to angle the x-axis text.

ggplot(mtcars, aes(mpg, disp)) + 
  geom_point(size = 3) + 
  theme_ifr() +
  theme(legend.position = c(1, 1),
        axis.text.x = element_text(angle = 45, 
                                   hjust = 1))

Colours

We have created two colour pallettes for use within ggplot2. The first colour palette (scale_colour_ifr or scale_fill_ifr) consists of six colours that are complementary to IFR's logo, which should be used for all plots with six or less colours. The second palette (scale_colour_ifr10 or scale_fill_ifr10) is a larger palette of 10 colourblind-friendly colours that is used whenever there are more than six colours in a plot (typically rare).

The custom palettes are applied like any other ggplot colour palette.

ggplot(mtcars, aes(as.factor(carb), fill = as.factor(carb))) + 
  geom_bar() + 
  scale_fill_ifr() +
  theme_ifr()

ChickWeight %>%
   mutate(Chick = as.factor(Chick)) %>%
   group_by(Chick) %>%
   summarise(Mean = mean(weight),
            .groups = 'drop') %>%
   slice(1:10) %>%
   ggplot(., aes(x = Chick, y = Mean, fill = Chick)) +
   geom_col() +
   scale_fill_ifr10() +
   theme_ifr() 

Viewing IFR Colours

A simple function (show_colour_ifr) was created to display the six custom colours and allow the user to select colours for a custom plot. For example, when overlaying multiple plot types or adding lines to plots, the user may want to select colours without applying the full palette.

show_ifr_colours()

ggplot(mtcars, aes(mpg, disp)) + 
  geom_point(size = 3) + 
  theme_ifr() +
  geom_vline(xintercept = 20, 
             size = 3,
             color = "#a40c01") +
  geom_hline(yintercept = 300,
             size = 3,
             color = "#104692")

Plotting Best Practices:

1. Use ggplot2 whenever possible
2. Save plots to file using ggsave:
3. Resolution should be set to 600 dpi
4. Scale the plot size using the inches argument
5. Typically save plots as 6 inches wide to fit the width of a 8.5 x 11 sheet
6. ggsave("plot.png", plot, height = 6, width = 6, units = "in", dpi = 600)
7. Do not use titles on plots
8. Always use legends rather than explaining the colours in the caption
9. Gridlines can be added if necessary for interpretation/clarity
10. E.g., panel.grid.major.x = element_line(size = 0.25)
11. Use commas or "K" if you numbers in the thousands as y-axis labels
12. E.g., using the scales package: scale_y_continuous(label = comma)
13. Angle your x-axis when necessary
14. theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1)
15. Don't use an x-axis label for time series data (e.g., dates or years)
16. Use the abbreviated month when plotting dates:
17. E.g., "2020-Jan-15", or "Jan-15" (if no year is required)

InStreamFisheries/IFRthemes documentation built on July 6, 2023, 3:24 p.m.