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rplotggplot2ape-phylo

how to make a PCA plots as I posted here

I know how to use the PCA results to draw the circle, but failed to draw the x.lab and the y.lab based on the plotting results from s.class.

How to make a plot as I posted here? two muppets I would like to ask more about this.

  1. How to make the points bigger or smaller according to another integer variable?

  2. Can ggplot2 draw the same circle as s.class? The previous answers do not show how to draw circles.

Solution

  • The size of the points cane adjusted using size. The ellipses can be added via stat_ellipsis

    pca <- prcomp(iris[iris$Species %in% c("virginica","versicolor"),1:4], retx = TRUE,  scale = TRUE,tol=0.4)
predicted <-predict(pca,iris[,1:4])
ggplot(data.frame(predicted))+aes(x=PC1,y=PC2,color=iris$Species)+geom_point(aes(size=iris$Sepal.Length))+stat_ellipse()+stat_ellipse(level=0.8)

    enter image description here