Joshua Grant Joshua Grant - 1 month ago 7
R Question

autoplot - How to adjust loading labels?

I would like to be able to adjust the positions of the loading labels, so that they do not fall atop the the arrows. However, I do not know where the adjustments need to be made. The

geom_text
can be used to adjust the position of the site positions, but I cannot find where the vectors are stored in
str(g)
.

library(ggplot2)
library(ggfortify)
df <- data.frame(replicate(10,sample(-10:10,10,rep=TRUE)))
names(df) <- c('up','down','left','right','circle','square','triangle','x','r1','l1')
rownames(df) <- paste('Dummy Site', seq(0,9,1))
g <- autoplot(prcomp(df[,-11], scale=TRUE), data=df,
loadings.label=TRUE, loadings=TRUE,
loadings.label.size=8, loadings.colour='blue',
label.size=5) +
geom_text(vjust=-1, label=rownames(df)) +
theme(plot.background=element_blank(),
panel.background=element_rect(fill='transparent',color='black',size=1),
legend.text=element_text(hjust=1),
legend.key=element_blank())
g


I've looked in
ggplot2::theme
and I've examined the help docs for
autoplot
, but can't find any mention of the adjusting label position. Bonus points if it can adjust based on the vector of the arrow, but a static adjustment would be acceptable.

Currently, here is what the plot looks like:
An example of what the above code generates

Answer

You can get the coordinates by layer_data(g, 2). But autoplot(prcomp.obj) passes other arguments to ggbiplot(), so you can change label and loadings.label position using arguments of ggbiplot(), such as loadings.label.hjust (see ?ggbiplot).

example code:
arrow_ends <- layer_data(g, 2)[,c(2,4)]

autoplot(prcomp(df[,-11], scale=TRUE), data=df,
         loadings.label=TRUE, loadings=TRUE, 
         loadings.label.size=8, loadings.colour='blue',
         label.size=5, loadings.label.vjust = 1.2) +     # change loadings.label position
     geom_point(data = arrow_ends, aes(xend, yend), size = 3) +  # the coordinates from layer_data(...)
     geom_text(vjust=-1, label=rownames(df)) +
     theme(plot.background=element_blank(),
           panel.background=element_rect(fill='transparent',color='black',size=1),
           legend.text=element_text(hjust=1),
           legend.key=element_blank()) 

enter image description here