Articles - ggpubr: Publication Ready Plots

ggplot2 - Easy Way to Change Graphical Parameters

|    |   48611  |  Comments (3)  |  ggpubr: Publication Ready Plots

This article describes the function ggpar() [in ggpubr], which can be used to simply and easily customize any ggplot2-based graphs. The graphical parameters that can be changed using ggpar() include:

  • Main titles, axis labels and legend titles
  • Legend position and appearance
  • colors
  • Axis limits
  • Axis transformations: log and sqrt
  • Axis ticks
  • Themes
  • Rotate a plot

Note that all the arguments accepted by the function ggpar() can be also directly passed to the plotting functions in ggpubr package, such as ggboxplot(), ggdotplot(), ggscatter(), …

Contents:

Prerequisites

Install ggpubr (version >= 0.1.4), for easily creating ggplot2-based publication ready plots.

Install from CRAN:

install.packages("ggpubr")

Or, install the latest developmental version from GitHub as follow:

if(!require(devtools)) install.packages("devtools")
devtools::install_github("kassambara/ggpubr")

Load ggpubr:

library(ggpubr)

Basic plots

We start by creating a basic box plot colored by groups. To add the panel border line, we’ll use the helper function border() [in ggpubr].

# Basic plot
p <- ggboxplot(ToothGrowth, x = "dose", y = "len",
               color = "dose")
p
# Add grids
p + grids(linetype = "dashed")

# Add panel border line
p + border("black")
  
# Change background color
p + bgcolor("#BFD5E3") +
  border("#BFD5E3")

Change titles and axis labels

Change plot titles and labels as follow:

# Change titles and axis labels
p2 <- ggpar(p, 
            title = "Box Plot created with ggpubr",
            subtitle = "Length by dose",
            caption = "Source: ggpubr",
            xlab ="Dose (mg)", 
            ylab = "Teeth length",
            legend.title = "Dose (mg)")
p2

Change the font/appearance of plot titles and labels. Use ggpar():

ggpar(p2, 
      font.title = c(14, "bold.italic", "red"),
      font.subtitle = c(10,  "orange"),
      font.caption = c(10,  "orange"),
      font.x = c(14,  "blue"),
      font.y = c(14,  "#993333")
      )

or, equivalently, use font():

p2 +
 font("title", size = 14, color = "red", face = "bold.italic")+
 font("subtitle", size = 10, color = "orange")+
 font("caption", size = 10, color = "orange")+
 font("xlab", size = 12, color = "blue")+
 font("ylab", size = 12, color = "#993333")

Note that, you can change simultaneously titles/labels text and appearance at once using the function ggpar() as follow:

# Change title texts and fonts
# line break: \n
ggpar(p, title = "Plot of length \n by dose",
      xlab ="Dose (mg)", ylab = "Teeth length",
      legend.title = "Dose (mg)",
      font.title = c(14,"bold.italic", "red"),
      font.x = c(14, "bold", "#2E9FDF"),
      font.y = c(14, "bold", "#E7B800"))

Note that,

  • font.title, font.subtitle, font.caption, font.x, font.y are vectors of length 3 indicating respectively the size (e.g.: 14), the style (e.g.: “plain”, “bold”, “italic”, “bold.italic”) and the color (e.g.: “red”) of main title, subtitle, caption, xlab and ylab, respectively. For example font.x = c(14, “bold”, “red”). Use font.x = 14, to change only font size; or use font.x = “bold”, to change only font face.

  • you can use line breaks, to split long title into multiple lines.

Change legend position & appearance

ggpar(p,
      legend = "right", legend.title = "Dose (mg)") + 
  font("legend.title", color = "blue", face = "bold")+ 
  font("legend.text", color = "red")

Note that, the legend argument is a character vector specifying legend position. Allowed values are one of c(“top”, “bottom”, “left”, “right”, “none”). To remove the legend use legend = “none”. Legend position can be also specified using a numeric vector c(x, y). Their values should be between 0 and 1. c(0,0) corresponds to the “bottom left” and c(1,1) corresponds to the “top right” position.

Change color palettes

Group colors

The argument palette (in ggpar() function ) can be used to change group color palettes. Allowed values include:

  • Custom color palettes e.g. c(“blue”, “red”) or c(“#00AFBB”, “#E7B800”);
  • “grey” for grey color palettes;
  • brewer palettes e.g. “RdBu”, “Blues”, …; To view all, type this in R: RColorBrewer::display.brewer.all().
  • and scientific journal palettes from ggsci R package, e.g.: “npg”, “aaas”, “lancet”, “jco”, “ucscgb”, “uchicago”, “simpsons” and “rickandmorty”.
# Use custom color palette
ggpar(p, palette = c("#00AFBB", "#E7B800", "#FC4E07"))
# Use brewer palette. 
# Type RColorBrewer::display.brewer.all(), to see possible palettes
ggpar(p, palette = "Dark2" )
# Use grey palette
ggpar(p, palette = "grey")
   
# Use scientific journal palette from ggsci package
# Allowed values: "npg", "aaas", "lancet", "jco", 
#   "ucscgb", "uchicago", "simpsons" and "rickandmorty".
ggpar(p, palette = "npg") # nature

Alternatively, you can use directly the functions color_palette() and fill_palette() [in ggpubr] as follow:

# jco color palette
p + color_palette("jco")
# Custom color
p + color_palette(c("#00AFBB", "#E7B800", "#FC4E07"))

Gradient colors

To change easily gradient colors, the ggpubr package provides the functions: gradient_color() and gradient_fill().

For example, start by creating a scatter plot colored according the values of a continuous variable “mpg”.

p3 <- ggscatter(mtcars, x = "wt", y = "mpg", color = "mpg",
                size = 2)

Change gradient color:

# Use one custom color
p3 + gradient_color("red")
# Two colors
p3 + gradient_color(c("blue",  "red"))
# Three colors
p3 + gradient_color(c("blue", "white", "red"))
# Use RColorBrewer palette
p3 + gradient_color("RdYlBu")

For gradient_fill(), the same syntax holds true. Start by creating a scatter plot filled by a continuous variable. Then, change the gradient color.

p4 <- ggscatter(mtcars, x = "wt", y = "mpg", fill = "mpg",
                size = 4, shape = 21)
p4 + gradient_fill(c("blue", "white", "red"))

Change axis limits and scales

The following arguments can be used in ggpar():

  • xlim, ylim: a numeric vector of length 2, specifying x and y axis limits (minimum and maximum values), respectively. e.g.: ylim = c(0, 50).
  • xscale, yscale: x and y axis scale, respectively. Allowed values are one of c(“none”, “log2”, “log10”, “sqrt”); e.g.: yscale=“log2”.
  • format.scale: logical value. If TRUE, axis tick mark labels will be formatted when xscale or yscale = “log2” or “log10”. 
# Change y axis limits
ggpar(p, ylim = c(0, 50))
# Change y axis scale to log2
ggpar(p, yscale = "log2")
# Format axis scale
ggpar(p, yscale = "log2", format.scale = TRUE)

Alternatively, you can also use the function xscale() and yscale() [in ggpubr], as follow:

p + yscale("log2", .format = TRUE)

Customize axis text and ticks

# Change the font of x and y axis texts.
# Rotate x and y texts, angle = 45
p + 
  font("xy.text", size = 12, color = "blue", face = "bold") +
  rotate_x_text(45)+       
  rotate_y_text(45)
# remove ticks and axis texts
p + rremove("ticks")+
  rremove("axis.text")

Rotate a plot

# Horizontal box plot
p + rotate()

Change themes

The default theme in ggpubr is theme_pubr(), for publication ready theme.

The argument ggtheme can be used in any ggpubr plotting functions to change the plot theme.

Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), etc. It’s also possible to use the function “+” to add a theme.

# Gray theme
p + theme_gray()
# Black and white theme
p + theme_bw()

# Theme light
p + theme_light()
# Minimal theme
p + theme_minimal()
# Empty theme
p + theme_void()

Remove ggplot components

The function rremove() [in ggpubr] can be used to remove a specific component from a ggplot.

Usage:

rremove(object)

Object: character string specifying the plot components. Allowed values include:

  • “grid” for both x and y grids
  • “x.grid” for x axis grids
  • “y.grid” for y axis grids
  • “axis” for both x and y axes
  • “x.axis” for x axis
  • “y.axis” for y axis
  • “xlab”, or “x.title” for x axis label
  • “ylab”, or “y.title” for y axis label
  • “xylab”, “xy.title” or “axis.title” for both x and y axis labels
  • “x.text” for x axis texts (x axis tick labels)
  • “y.text” for y axis texts (y axis tick labels)
  • “xy.text” or “axis.text” for both x and y axis texts
  • “ticks” for both x and y ticks
  • “x.ticks” for x ticks
  • “y.ticks” for y ticks
  • “legend.title” for the legend title
  • “legend” for the legend

Examples:

# Basic plot
p <- ggboxplot(ToothGrowth, x = "dose", y = "len",
  ggtheme = theme_gray())
p
# Remove all grids
p + rremove("grid")
# Remove only x grids
p + rremove("x.grid")