ggplot2 scale_x_log10() destroys/doesn't apply for function plotted via stat_function()

Question

I finally managed to plot my custom fitted function over my data in ggplot2 but when I log-transform the x axis the plotted function gets totally messed up. It looks like th

Answer 1

Proposed Solution

The following code is one way to get ggplot2 to do what I think you are trying to accomplish.

library(ggplot2)

# Define function. Fitted parameters included as default values.
HillFunction = function(x, ec50=0.01, hill=0.7, rmax=1.0) {
    result = rmax / (1 + (ec50 / x)^hill)
    return(result)
} 

# Create x such that points are evenly spread in log space.
x = 10^seq(-5, 5, 0.2) 
y_fit = HillFunction(x)
y_raw = y_fit + rnorm(length(y_fit), sd=0.05)

dat = data.frame(x, y_fit, y_raw)

plot_1 = ggplot(data=dat, aes(x=x, y=y_raw)) +
         geom_point() +
         geom_line(data=dat, aes(x=x, y=y_fit), colour="red") +
         scale_x_log10() +
         opts(title="Figure 1. Proposed workaround.")

png("plot_1.png", height=450, width=450)
print(plot_1)
dev.off()

Problems With stat_function()

1. stat_function() is trying to evaluate HillFunction() for negative values of x. This why you get the missing values error.

2. stat_function() is not evaluating HillFunction() for any x values between 0 and 1. It is selecting x in linear space, ignoring that scale_x_log10() has been specified.

The following code illustrates the problem, but I still can't explain why stat_function() diverges so much from y_fit in Figure 2.

plot_2 = ggplot(dat, aes(x=x, y=y_fit)) +
         geom_point() +
         stat_function(fun=HillFunction, colour="red") +
         scale_x_log10() +
         opts(title="Figure 2. stat_function() misbehaving?")

png("plot_2.png", height=450, width=450)
print(plot_2)
dev.off()


png("plot_3.png", height=450, width=450)

plot(x, y_fit, pch=20, log="x")
curve(HillFunction, col="red", add=TRUE)
title("Figure 3. curve() behaving as expected.")

dev.off()