Search code examples
rggplot2pca

How to get a PCA plot with PC3 and PC4 with ggbiplot

I need some help to get PC3 and PC4 for my data.

**library(ggbiplot)
iris<- read.csv("PCA2_umar.csv")
log.ir <- log(iris[, 1:8])
ir.species <- iris[, 9]

ir.pca <- prcomp(log.ir, center = TRUE, scale. = TRUE)

ggbiplot(ir.pca, obs.scale = 1, var.scale = 1, groups = ir.species, alpha = 0) +
  theme(legend.direction = 'vertical', legend.position = 'right') + 
  scale_color_manual(values=c("Black", "Black")) +
  scale_fill_manual(values = c("#FF8000", "#0080FF")) + # just offset by one to show
  geom_point(size = 3, shape = 21, aes(fill = groups, color = groups))**

PS. Also how can I show the two groups with different symbol. I need to show one of the group with "Dot in a circle" symbol style. Many thanks Link to Excel data

Solution

  • By including ggbiplot(ir.pca, choices = c(3,4), obs.scale.... we can get PC3 and PC4.