Plotting PCA biplot with autoplot: modify arrow thickness

Question

I am using the autoplot function from ggfortify as illustrated by the code below using iris.pca. This example only has three variables (hence 3 loadings) but my data set has a lot more variables so I wish I could reduce the size of the arrows to make the plot more readable. I think the default size is 1 pt and I'd like to get it down to something like 0.5. Although there are arguments to modify the loadings color and label size, I could not find a way to adjust the thickness of the arrows. Does anyone knows how to do this?

library(ggplot2)
library(ggfortify)

df <- iris[c(1, 2, 3, 4)]
iris.pca<-(prcomp(df))

autoplot(iris.pca, data=iris, colour="Species", loadings=TRUE, loadings.colour = "black")+
  scale_colour_manual(values=c("forestgreen","red","blue"))+
  scale_fill_manual(values=c("forestgreen","red","blue"))+
  scale_shape_manual(values=c(25,22,23))+
  theme_bw()

Hello, please provide a reproducible example so we can all see what you are trying to do with `iris.pca`. — Stanislaus Stadlmann, Oct 04 '18 at 13:54
I edited my question. The example using `iris.pca` is just to illustrate what plot I am talking about. In my case I have more variables and I feel reducing the thickness of the arrows would help readability. — Drosof, Oct 04 '18 at 19:21

score 5 · Accepted Answer · answered Oct 05 '18 at 08:56

The problem is that ggfortify has already created a ggplot2 object. So if you don't want to recreate the plot by hand (which would be the cleaner solution here), you have to modify the existing plot in the following way:

Old code

library(ggplot2)
library(ggfortify)

df <- iris[c(1, 2, 3, 4)]
iris.pca<-(prcomp(df))

d <- autoplot(iris.pca, data=iris, colour="Species", loadings=TRUE, loadings.colour = "black", scale = 1)+
  scale_colour_manual(values=c("forestgreen","red","blue")) +
  scale_fill_manual(values=c("forestgreen","red","blue")) +
  scale_shape_manual(values=c(25,22,23))+
  theme_bw()

Modifications

d$layers[[2]]$aes_params$size <- 0.5
d$layers[[2]]$geom_params$arrow$length <- unit(6, units = "points")
d

This essentially manually creates the size aesthetic for the arrow lines, and shrinks the pointy ends of the arrows:

"Length" refers to the size of the arrowhead. If you make the lines thinner, for visual completeness you should also make the arrowheads smaller. — Stanislaus Stadlmann, Oct 05 '18 at 09:28
Don’t know how I overlooked the `size` — thanks for the clarification! — Roman, Oct 05 '18 at 11:13

Plotting PCA biplot with autoplot: modify arrow thickness

1 Answers1

Old code

Modifications