Methods ggplot2 Guide

Alexis Provencal

Introduction

This is a guide to making plots using ggplot2 and ggpubr in Methods! You may be familiar with theme_minimal() or theme_classic() for ggplot2, this function works in the same way. Just copy and paste the function chunk to your R Markdown and use when needed.

There are many aesthetic requirements for data visualizations in Methods. This theme only meets some of them because in ggplot2, the theme() function is only used to customize the non-data elements of a plot.

Note: this theme only works with ggplot2 and ggpubr plots and the function needs to be in your markdown to use it.

Aesthetic requirements the function meets:

• All theme elements are black and white
• No lines around plot or grid lines, only black axes lines
• Same font as the paper the plot will be included in, so font is an argument of the function
• Axis labels must be very large, so size of them can be manually altered in the function

The function takes the following arguments:

• font = "nameOfFont" default = NA, see next section for font names you can use.
• base_size = n default = 12, this will be the size of the produced text.

Fonts

There are font options that are available in base R. The most relevant are "Times" and "sans", which are Times New Roman and Arial respectively. There are many other font options, but libraries must be installed.

Aesthetic requirements the function does not meet:

• Bars in bar graphs must touch the axis: add scale_y_continuous(expand = c(0, 0)) to your ggplot for vertical bar plot, and scale_x_continuous(expand = c(0, 0)) to your ggplot for a horizontal bar plot.
• The color of points, bars, etc. must be black: specify in geom_bar() with fill = "black" or geom_point with color = "black".
• The p-value and test statistics must be displayed: create objects for your p_value and test_statistic and use annotate() to do add them to your plot.
• All elements of the plot must be the same font: when you add text with annotate() or stat_compare_means(), you have to specify family = "nameOfFont" and size = n inside each element you add.

The function:

library(ggplot2)

methodsTheme = 
  function(font = NA, base_size = 12){
  theme(
    #Text font
    text = element_text(family = font, size = base_size),
    
    #Color
    line = element_line(color = "black"),
    panel.background = element_rect(fill = "white"), #fill plot background
    legend.key = element_rect(fill = "white"), #fill background of legend key
    axis.line = element_line(color = "black"), #color axes lines
    
    #Positioning
    legend.position = "right", #change legend position
      #options: none, left, right, bottom, top
    
    #Text sizes and options
    plot.title = element_text(
      size = base_size*1.3, #title size
      face = "plain"), #options: plain, italic, bold, bold.italic
    axis.title = element_text(size = base_size), #axis titles text size
    axis.text = element_text(size = base_size, color = "black"), #axis labels/tick numbers text size
    legend.text = element_text(size = base_size), #legend text size
    legend.title = element_text(size = base_size) #legend title text size
  )
}

Note: the name of the function can be changed from methodsTheme to anything you please! And, any other aspect of the function can be changed. Use ChatGPT or look at the documentation for assistance in changing the function preform how you would like.

How to use the function?

The function takes in two arguments font and base_size. If base_size is not specified, it will default to 12 pt. To use the function:

ggplot(data, aes(x = Species, y = meanSepalLength)) +
  geom_bar(stat = "identity", position = "dodge", fill = "black", #fill black
           width = 0.7) + #changes width of bars
  labs(x = "Species",
       y = "Mean Sepal Length") +
  scale_y_continuous(expand = c(0, 0)) + #makes bars touch axis
  methodsTheme(font = "Times", base_size = 24) #using custom theme

How do functions work?

Functions take in arguments and return something. In this case, the function takes in the arguments font and base_size and returns a theme that you can add to your ggplot. You can see the arguments of a function and their default values here: function(font = NA, base_size = 12){}. Arguments have default values so that they run without the user needing to specify them. But, beware that you will need to specify arguments to fully take advantage of the capabilities of this function.

ggpubr

library(ggplot2)
library(ggpubr)
library(ggsignif)

myfont = "Times"

# Create a ggviolin plot with ggpubr
ggviolin(iris, x = "Species", y = "Sepal.Length", fill = "gray") +
  labs(x = "Species",
       y = "Sepal Length") +
  geom_boxplot(width = 0.2, fill = "white", color = "black") +
  stat_compare_means(method = "anova", family = myfont, size = 8) +
  methodsTheme(font = myfont, base_size = 24)