R: ggfortify: "Objects of type prcomp not supported by autoplot"

r pca ggfortify
JR Flanders picture JR Flanders · May 5, 2015 · Viewed 18.8k times · Source

I am trying to use ggfortify to visualize the results of a PCA I did using prcomp.

sample code: 

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

Error: Objects of type prcomp not supported by autoplot. Please use qplot() or ggplot() instead.

What is odd is that autoplot is specifically designed to handle the results of prcomp - ggplot and qplot can't handle objects like this. I'm running R version 3.2 and just downloaded ggfortify off of github this AM.

Can anyone explain this message?

Answer

Konrad picture Konrad · May 5, 2015

I'm guessing that you didn't load the required libraries, the code below:

library(devtools)
install_github('sinhrks/ggfortify')
library(ggfortify); library(ggplot2)
data(iris)
iris.pca <- iris[c(1, 2, 3, 4)] 
autoplot(prcomp(iris.pca))

will work enter image description here

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