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Graphical options

Source: vignettes/web/options.rmd
options.rmd

visreg tries to set up pleasant-looking default options, but everything can be tailored to user specifications. For the plots below, we work from this general model:

airquality$Heat <- cut(airquality$Temp, 3, labels=c("Cool", "Mild", "Hot"))
fit <- lm(Ozone ~ Solar.R + Wind + Heat, data=airquality)

Turning on/off plot components

By default, visreg includes the fitted line, confidence bands, and partial residuals, but the residuals and the bands can be turned off:

visreg(fit, "Wind", band=FALSE)

visreg(fit, "Wind", partial=FALSE)

Note that by default, when you turn off partial residuals, visreg tries to display a rug so you can at least see where the observations are. You can turn this off too:

visreg(fit, "Wind", partial=FALSE, rug=FALSE)

Finally, there is an option for displaying separate rugs for positive and negative residuals on the top and bottom axes, respectively, with rug=2 (this is particularly useful for logistic regression):

visreg(fit, "Wind", rug=2, partial=FALSE)

Jittering

If there are many ties in a numeric variable x, jittering can be helpful way to avoid overplotting:

fit <- lm(Ozone ~ Solar.R + Wind + poly(Month, 2), data=airquality)
visreg(fit, "Month")

visreg(fit, "Month", jitter=TRUE)

Appearance of points, lines, and bands

Specifying col='red' won’t work, because visreg can’t know whether you’re trying to change the color of the line, the band, or the points. These options must be specified through separate parameters lists:

  • line.par: Controls the appearance of the fitted line
  • fill.par: Controls the appearance of the confidence band
  • points.par: Controls the appearance of the partial residuals

Each of these can be abbreviated, as in the example below:

visreg(fit, "Wind", line=list(col="red"),
                    fill=list(col="green"),
                    points=list(cex=1.5, pch=1))

Generic plot options

Other options get passed along to plot, so any option that you could normally pass to plot, like main, will work fine. Here’s an example that includes a bunch of options like this:

fit <- lm(log(Ozone) ~ Solar.R + Wind + Temp, data=airquality)
visreg(fit, "Wind", yaxt="n", main="Ozone is bad for you", bty="n", ylab="Ozone")
at <- seq(1.5, 5, 0.5)
lab <- round(exp(at), 1)
axis(2, at=at, lab=lab, las=1)

Whitespace for factors

When x is a factor, the whitespace option controls the amount of whitespace in between the categories:

fit <- lm(Ozone ~ Solar.R + Wind + Heat, data=airquality)
par(mfrow=c(1,2))
visreg(fit, "Heat", whitespace=.1)
visreg(fit, "Heat", whitespace=.5)

Subsetting the plot

Occasionally, you might want to plot only a subset of the levels or observations; you can use subset to accomplish this:

v <- visreg(fit, "Wind", by="Heat", plot=FALSE)
v1 <- subset(v, Heat %in% c("Cool", "Hot"))
plot(v1)

v2 <- subset(v, Wind < 15)
plot(v2, layout=c(3,1))