Alex Rivera | Logout

In ggplot restrict y to be >0 in LOESS

Asked 2010-05-05T21:51:12.030
17

Here's my code:

#data
sites <- 
  structure(list(site = c(928L, 928L, 928L, 928L, 928L, 928L, 928L,
                          928L, 928L, 928L, 928L, 928L, 928L, 928L,
                          928L, 928L, 928L, 928L, 928L, 928L, 928L,
                          928L, 928L, 928L, 928L, 928L), 
                 date = c(13493L, 13534L, 13566L, 13611L, 13723L,
                          13752L, 13804L, 13837L, 13927L, 14028L,
                          14082L, 14122L, 14150L, 14182L, 14199L,
                          16198L, 16279L, 16607L, 16945L, 17545L,
                          17650L, 17743L, 17868L, 17941L, 18017L, 18092L),
                 y = c(7L, 7L, 17L, 18L, 17L, 17L, 10L, 3L, 17L, 24L, 
                       11L, 5L, 5L, 3L, 5L, 14L, 2L, 9L, 9L, 4L, 7L,
                       6L, 1L, 0L, 5L, 0L)), 
            .Names = c("site", "date", "y"),
            class = "data.frame", row.names = c(NA, -26L))

#convert to date
x<-as.Date(sites$date, origin="1960-01-01") 

#plot smooth, line goes below zero!
qplot(data=sites, x, y, main="Site 349") 
(p <- qplot(data = sites, x, y, xlab = "", ylab = ""))
(p1 <- p + geom_smooth(method = "loess",span=0.5, size = 1.5))

Some of the LOESS lines and confidence intervals go below zero, I would like to restrict the graphics to 0 and positive numbers (because negative do not make sense). enter image description here

How can I do this?

r plot ggplot2 axis
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1 Answer

17

I am seconding Matt Parker's suggestion that you have to change the fitting procedure. One option that often works for positive-only data, is to do the fit on log-scale, and then exponentiate to get results on the original scale. This will guarantee positive only values.

Generating random data that has some of this issues:

 d <- data.frame(x=0:100)
 d$y <- exp(rnorm(nrow(d), mean=-d$x/40, sd=0.8))
 qplot(x,y,data=d) + stat_smooth()

Now we can use ggplot's transformation capabilites to log-transform the y-values, but display the results on an exponential scale (which corresponds to the original one):

qplot(x,y,data=d) + stat_smooth() + scale_y_log10()+coord_trans(ytrans="pow10")

You can see examples like this on the coord_trans help page. If you don't like the y-axis, you can manipulate the breaks and labels.

EDIT based on the question update

There have been some changes in ggplot2 since the question was originally asked, and the original answer did not deal with 0's.

Option 1

The main idea of the solution is the same: find a transformation that will map the range of possible values to -Inf to Inf, do the loess smooth there, and then backtransform the result. The log-transformation would be great if there were no zeroes. I don't think the required function exists if 0 is included, but a possibility that often works is the log(1+x) transformation. That is built-in, but we need to have the inverse transformation exp(x)-1 as well.

library(scales)
#create exp(x)-1 transformation, the inverse of log(1+p)
expm1_trans <-  function() trans_new("expm1", "expm1", "log1p")

qplot(x, y, data=sites) + stat_smooth(method="loess") +
  scale_y_continuous(trans=log1p_trans()) +
  coord_trans(ytrans=expm1_trans())

answered 2010-05-06T15:40:07.863

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