R – Ignore outliers in ggplot2 boxplot

ggplot2r

How would I ignore outliers in ggplot2 boxplot? I don't simply want them to disappear (i.e. outlier.size=0), but I want them to be ignored such that the y axis scales to show 1st/3rd percentile. My outliers are causing the "box" to shrink so small its practically a line. Are there some techniques to deal with this?

Edit
Here's an example:

y = c(.01, .02, .03, .04, .05, .06, .07, .08, .09, .5, -.6)
qplot(1, y, geom="boxplot")

Best Answer

Use geom_boxplot(outlier.shape = NA) to not display the outliers and scale_y_continuous(limits = c(lower, upper)) to change the axis limits.

An example.

n <- 1e4L
dfr <- data.frame(
  y = exp(rlnorm(n)),  #really right-skewed variable
  f = gl(2, n / 2)
)

p <- ggplot(dfr, aes(f, y)) + 
  geom_boxplot()
p   # big outlier causes quartiles to look too slim

p2 <- ggplot(dfr, aes(f, y)) + 
  geom_boxplot(outlier.shape = NA) +
  scale_y_continuous(limits = quantile(dfr$y, c(0.1, 0.9)))
p2  # no outliers plotted, range shifted

Actually, as Ramnath showed in his answer (and Andrie too in the comments), it makes more sense to crop the scales after you calculate the statistic, via coord_cartesian.

coord_cartesian(ylim = quantile(dfr$y, c(0.1, 0.9)))

(You'll probably still need to use scale_y_continuous to fix the axis breaks.)

Any ggplots side-by-side (or n plots on a grid)

The function grid.arrange() in the gridExtra package will combine multiple plots; this is how you put two side by side.

require(gridExtra)
plot1 <- qplot(1)
plot2 <- qplot(1)
grid.arrange(plot1, plot2, ncol=2)

This is useful when the two plots are not based on the same data, for example if you want to plot different variables without using reshape().

This will plot the output as a side effect. To print the side effect to a file, specify a device driver (such as pdf, png, etc), e.g.

pdf("foo.pdf")
grid.arrange(plot1, plot2)
dev.off()

or, use arrangeGrob() in combination with ggsave(),

ggsave("foo.pdf", arrangeGrob(plot1, plot2))

This is the equivalent of making two distinct plots using par(mfrow = c(1,2)). This not only saves time arranging data, it is necessary when you want two dissimilar plots.

Appendix: Using Facets

Facets are helpful for making similar plots for different groups. This is pointed out below in many answers below, but I want to highlight this approach with examples equivalent to the above plots.

mydata <- data.frame(myGroup = c('a', 'b'), myX = c(1,1))

qplot(data = mydata, 
    x = myX, 
    facets = ~myGroup)

ggplot(data = mydata) + 
    geom_bar(aes(myX)) + 
    facet_wrap(~myGroup)

Update

the plot_grid function in the cowplot is worth checking out as an alternative to grid.arrange. See the answer by @claus-wilke below and this vignette for an equivalent approach; but the function allows finer controls on plot location and size, based on this vignette.

Rotating and spacing axis labels in ggplot2

Change the last line to

q + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))

By default, the axes are aligned at the center of the text, even when rotated. When you rotate +/- 90 degrees, you usually want it to be aligned at the edge instead:

alt text

The image above is from this blog post.

Best Answer

Related Solutions

R – Side-by-side plots with ggplot2

Any ggplots side-by-side (or n plots on a grid)

Appendix: Using Facets

Update

Rotating and spacing axis labels in ggplot2

Related Topic