## load packages
library("gclus")
library("stats")
library("cluster")
library("clusterSim")

# set working directory for module and check
setwd("C:/Users/ufrei/Desktop/WD-module")
getwd()

#load the MeanMeanEarPhenotypes dataset and look at the structure
data <- read.csv("MeanMeanEarPhenotypes.csv", header = T)
str(data)


#subsetting dataset to 5 variables
#datap <- subset(data, select=c("RowNo.","EarDM","EarL", "CobWt", "ca300KWt"  ))
datap <-subset(data, select= -(Pedigree:Type)
# and data standardization
PCAdata <-data.Normalization(datap, type="n1")


cpairs(PCAdata)

PCA2 <- prcomp(PCAdata, center=T, scale=T)
class(PCA2)
ls(PCA2)
summary(PCA2)

#calculate Eigen values for each component: square of standard deviation
PCA2$sdev^2
# Graphical display
screeplot(PCA2, type="line", main="Scree Plot")

#graphical display:
biplot(PCA2,cex =c(1, 0.7) )
biplot(PCA2,cex =c(1, 0.7),xlabs=data$Type )

var <- varimax(PCA2$rotation)
var