How do you force Rmarkdown plots to be Square instead of Rectangle?

Question

I have a Generalized Linear Model (GLM) that I'm plotting diagnostics for using the glm.diag.plots function in the MASS package. But it tends to plot rectangular instead of square, which is very ugly for publication.

Below is some sample code that shows the problem in an .Rmd file. In Rstudio, you can just drag the window around until it's square, but not possible in Rmarkdown documents, and I'd like to enforce square manually.

I checked in the ggplot documentation for ways to enforce square plotting, but could not find anything. glm.diag.plot() appears to use split.screen(), which doesn't provide any documentation for enforcing aspect ratios, either.

Answer 1

@rawr's comment is spot-on; this is a knitr/markdown issue, not glm.diag or ggplot or anything else. All you need to do is specify the desired height and width of the output (in inches, by default) using fig.width and fig.height.

Answer 2

It looks like you are using glm.diag.plots from package boot to acquire plots. You could recreate them using ggplot if you wish. Here is an example:

some model:

data(anorexia, package = "MASS")

anorex.1 <- glm(Postwt ~ Prewt + Treat + offset(Prewt),
                family = gaussian, data = anorexia)

the glm.diag.plots output

library(boot)
glm.diag.plots(anorex.1)

To create each plot in ggplot first get an object from glm.diag.plots

z <- glm.diag.plots(anorex.1, ret = T)

then plot each plot:

library(ggplot2)

plot1 <- ggplot(data.frame(x = predict(anorex.1),
                           y = z$res))+
  geom_point(aes(x, y)) +
  xlab("Linear predictor") +
  ylab("Residuals") +
  theme_bw()+
  theme(aspect.ratio=1)

plot2 <- ggplot(data.frame(x = qnorm(ppoints(length(z$rd)))[rank(z$rd)],
                           y = z$rd)) +
  geom_point(aes(x, y)) +
  xlab("Ordered deviance residuals") +
  ylab("Quantiles of standard normal") +
  geom_abline(intercept = 0, slope = 1, lty =2) +
  theme_bw()+
  theme(aspect.ratio=1)

plot3 <- ggplot(data.frame(x = z$h/(1-z$h),
                           y = z$cook)) +
  geom_point(aes(x, y)) +
  xlab("h/(h-1)") +
  ylab("Cook statistic") +
  theme_bw()+
  theme(aspect.ratio=1)

plot4 <- ggplot(data.frame(x = 1:length(z$cook),
                           y = z$cook)) +
  geom_point(aes(x, y)) +
  xlab("Case") +
  ylab("Cook statistic") +
  theme_bw()+
  theme(aspect.ratio=1)

then combine them

library(cowplot)

plot_grid(plot1, plot2, plot3, plot4, ncol = 2)

Now you can customize each plot the way you wish.