########################################################
#################### TA13 - PCA ########################
########################################################

# Making sure the relevant packages are installed and loaded
if(!(c("factoextra") %in% rownames(installed.packages()))) {install.packages("factoextra")}

library(factoextra)


# Part 1 - 2D example
# ------------------------------------------------------------------------
Data <- read.csv("TA13.csv", header = F)
plot(Data, xlim = c(-10,10), ylim = c(-10,10), col = 'blue')

p <- prcomp(Data, scale. = F)

fviz_screeplot(p)
summary(p)

fviz_pca_ind(p, geom = "point")
plot(p$x[,1:2], xlim = c(-10,10), ylim = c(-10,10), col = 'blue')

fviz_pca_var(p)

# Part 2 - Lymphoma Data
# ------------------------------------------------------------------------
# Q1
lymphoma <- read.csv("lymphoma.csv", header = T)

# Q2
p <- prcomp(lymphoma[,-1], scale.=T)
fviz_pca_ind(p, geom = "point")
fviz_screeplot(p)
summary(p)

# Q3
loadings = p$rotation
barplot(loadings[,1], las=2)
fviz_pca_var(p)

# Q4
p$x

# Q5
fviz_pca_ind(p, geom = "point", col.ind = lymphoma$Result, pointsize = 2)

# Q6
fviz_pca_ind(p, geom = "point", axes = c(2,3),
             col.ind = lymphoma$Result, pointsize = 2)

# Q7
p <- prcomp(lymphoma[,-1], scale. = F)
fviz_pca_ind(p, geom = "point")
loadings = p$rotation
barplot(loadings[,1], las=2)
fviz_screeplot(p)
fviz_pca_ind(p, geom = "point", col.ind = lymphoma$Result, pointsize = 2)