3 Easy Ways to Create a GGPlot with Log Scale

13 Nov

GGPlot Log Scale Transformation

This article describes how to create a ggplot with a log scale. This can be done easily using the ggplot2 functions scale_x_continuous() and scale_y_continuous(), which make it possible to set log2 or log10 axis scale. An other possibility is the function scale_x_log10() and scale_y_log10(), which transform, respectively, the x and y axis scales into a log scale: base 10.

Note that, the scale functions transform the data. If you fit anything to the data it would probably change the fitted values.

An alternative is to use the function coord_trans() for transformed Cartesian coordinate system. coord_trans() is different to scale transformations in that it occurs after statistical transformation and will affect only the visual appearance of geoms.

In this R graphics tutorial, you will learn how to:

Log transform x and y axes into log2 or log10 scale
Show exponent after the logarithmic changes by formatting axis ticks mark labels.
Display log scale ticks. R function: annotation_logticks()

Contents:

Key ggplot2 R functions
Set axis into log2 scale
Set axis into log10 scale
Display log scale ticks mark
Conclusion

Key ggplot2 R functions

Start by creating a scatter plot using the cars data set:

library(ggplot2)
p <- ggplot(cars, aes(x = speed, y = dist)) + 
  geom_point()
p

R functions to set a logarithmic axis:

p + scale_x_log10(), p + scale_y_log10() : Plot x and y in log 10 scale, respectively.
p + coord_trans(x = “log2”, y = “log2”): Transformed cartesian coordinate system. Possible values for x and y are “log2”, “log10”, “sqrt”, …
p + scale_x_continuous(trans = “log2”), p + scale_y_continuous(trans = “log2”). Allowed value for the argument trans, include also ‘log10’.
p + scale_y_log10() + annotation_logticks(): Display log scale ticks.

Set axis into log2 scale

Log2 transformation of x and y axes
Format ticks label to show exponents

# Possible values for trans : 'log2', 'log10','sqrt'
p + scale_x_continuous(trans = 'log2') +
  scale_y_continuous(trans = 'log2')

# Format y axis tick mark labels to show exponents
require(scales)
p + scale_y_continuous(trans = log2_trans(),
    breaks = trans_breaks("log2", function(x) 2^x),
    labels = trans_format("log2", math_format(2^.x)))

Set axis into log10 scale

The following R code changes the y axis scale into log10 scale using the function scale_y_log10():

p + scale_y_log10()

Alternatively, you can use the function scale_y_continuous(), which allows to transform breaks and the format of labels.

p + scale_y_continuous(trans = "log10")

Display log scale ticks mark

Note that, log scale ticks make sense only for log scale base 10.

Key function: annotation_logticks() Data: Animals data sets, from the package MASS

Create a log-log plot without log scale ticks:

# Load packages
require(MASS) # to access Animals data sets
require(scales) # to access break formatting functions
data(Animals) # load data

# x and y axis are transformed and formatted
p2 <- ggplot(Animals, aes(x = body, y = brain)) + geom_point() +
     scale_x_log10(breaks = trans_breaks("log10", function(x) 10^x),
              labels = trans_format("log10", math_format(10^.x))) +
     scale_y_log10(breaks = trans_breaks("log10", function(x) 10^x),
              labels = trans_format("log10", math_format(10^.x))) +
     theme_bw() 
p2

Show log scale ticks:

p2 + annotation_logticks()

Note that, default log ticks are on bottom and left. To specify the sides of the log ticks :

# Log ticks on left and right
p2 + annotation_logticks(sides="lr")

# All sides
p2+annotation_logticks(sides="trbl")

Allowed values for the argument sides are the combination of “t” (top), “r” (right), “b” (bottom), “l” (left).

Conclusion

We introduce how to create a ggplot with log scale. Briefly, the steps are as follow:

Create an example of ggplot:

library(ggplot2)
p <- ggplot(cars, aes(x = speed, y = dist)) + 
  geom_point()

Log transformation of the axis scale:

 # log base 2 scale
p + scale_x_continuous(trans = 'log2') +
  scale_y_continuous(trans = 'log2')

# Log base 10 scale + log ticks (on left and bottom side)
p + scale_x_continuous(trans = 'log10') + 
  scale_y_continuous(trans = 'log10')+
  annotation_logticks(sides="lb")