[R] plots on log="y" scale with smooths
Michael Friendly
friendly at yorku.ca
Wed Sep 17 22:34:18 CEST 2014
In the following example, I am trying to plot a response on a log scale,
and add one or more smoothed
curves, e.g., lowess and abline. In base graphics, I'd like to do this
using log="y", so that the Y axis is
spaced on the log scale, but labeled as the actual response values.
Using ggplot2, I'm using
scale_y_log10 to achieve the same purpose. However, my attempts to add
the smooths differ
considerably, so I must be missing something.
Here's the data I'm working with for one example:
data("CodParasites", package = "countreg")
## omit NAs in response & predictor
CodParasites <- subset(CodParasites, !(is.na(intensity) | is.na(length)))
## plot only positive values of intensity
CPpos <- subset(CodParasites, intensity>0)
Here's the base graphics plot. The abline() is clearly wrong and the
lowess smooth looks too low.
How does one meld plots using log="y" with such additional plot
annotations ?
plot(jitter(intensity) ~ length, data = CPpos, log = "y")
with(CPpos, lines(lowess(length, log(intensity)), col="red", lwd=2) )
abline(lm(log(intensity) ~ length, data=CPpos))
Here's an attempt at a ggplot2 version, that actually looks more
reasonable, but I'm not sure that it
is correct:
library(ggplot2)
ggplot(CPpos, aes(x=length, y=intensity)) +
geom_jitter(position=position_jitter(height=.1), alpha=0.25) +
scale_y_log10(breaks=c(1,2,5,10,20,50,100, 200)) +
stat_smooth(method="loess", color="red", size=1.5) +
stat_smooth(method="lm")
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept. & Chair, Quantitative Methods
York University Voice: 416 736-2100 x66249 Fax: 416 736-5814
4700 Keele Street Web:http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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