R ggplot2 - Simple plot- cannot specify log axis limits

Question

I'm trying to create a simple densityplot in R in ggplot2. Here's my code which works great.

d <-  ggplot(result, aes(x=result$baseMeanA)) 
d + geom_density(colour="darkgreen", size=2, fill="darkgreen") + 
scale_x_log10() + scale_y_continuous(limits = c(0, 0.45))

The problem is that I cannot adjust the x-axis as I would like, into negative numbers.

scale_x_log10(limits= c(1, 10000))

works great, but

scale_x_log10(limits= c(-1, 10000))

does not work at all! It gives me this error:

Error in if (zero_range(range)) { : missing value where TRUE/FALSE needed

Please help!

Just guessing, but perhaps you want the limits on the original scale to go from 0.1 to 10000 (i.e. log10(x) goes from -1 to 5) ? Presumably you don't want log10(x) to go from -1 to 10000, because the upper limit would then be at 10^10000 (a very large value, since there are about 10^80 atoms in the observable universe en.wikipedia.org/wiki/Observable_universe ... ) If I'm right, then you want scale_x_log10(limits=c(0.1,1e5)) — Ben Bolker
– Ben Bolker, Commented Sep 17, 2012 at 18:38
Yes I think I understand now. I can't use negative numbers in a log scale.. Thank you. I see now what I need to do, I need to add a pseudonumber like 1 or 0.1 to the result, so that it visually will look correct, otherwise I will loose all the very small numbers somehow. — user1678000
– user1678000, Commented Sep 18, 2012 at 8:27

Sven Hohenstein · Accepted Answer · 2012-09-17 18:33:00Z

5

If the range of the limits should be partly below zero, you could log10-transform your variable and specify the limits for a continuous scale:

ggplot(result, aes(x=log10(baseMeanA))) +
   geom_density(colour="darkgreen", size=2, fill="darkgreen") + 
   scale_x_continuous(limits = c(-1, 10000) + 
   scale_y_continuous(limits = c(0, 0.45)) +

answered Sep 17, 2012 at 18:33

Sven Hohenstein

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Comments

Gavin Simpson · Accepted Answer · 2012-09-17 15:34:09Z

2

What you are trying to do doesn't make much sense does it? The log of negative numbers isn't something we can represent in R

R> log(-1)
[1] NaN
Warning message:
In log(-1) : NaNs produced

so where should R draw the axis to?

answered Sep 17, 2012 at 15:34

Gavin Simpson

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1 Comment

user1678000 Over a year ago

Yes, you are right probably. I did not know that. I think I know now that to solve my problem I need to add a pseudonumber to my result so that I visually can look at it.

JAponte · Accepted Answer · 2012-10-12 12:35:23Z

1

e^y cannot be negative. The exponential constant e is positive, and y is just an exponent. and by mathematical definition:

log(x) = y <==> x = e^y

This is precisely why R cannot calculate log(x) if x is negative. It just goes against the math definition.

I hope this helps understanding why this plot is giving you trouble.

answered Oct 12, 2012 at 12:35

JAponte

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