####################################################################################################################
######################       Scatter Plots - symbols, lines, legends             ###################################
####################################################################################################################

data(Puromycin)
attach(Puromycin)

#### DATA DESCRIPTION
help(Puromycin)
# Rate represents the instantaneous reaction rates(counts/min/min) 
# Conc repressents the substrate concentrations (ppm) 
# State represents the cell treatment (Puromycin - antibiotic inhibiting translation)

### SIMPLE HISTOGRAM OF REACTION RATE

hist(rate,breaks=20,freq=FALSE)
lines(density(rate),col="red",lwd=2)


### INDEX PLOT
plot(rate)

### TWO-VARIABLES PLOT
plot(rate~conc,data=Puromycin)

### CHANGE THE LIMITS OF THE AXIS
plot(rate~conc,data=Puromycin,xlim=c(0,1.2),ylim=c(45,210))

### CHANGE THE LABELS AND THE FONT SIZE
plot(rate~conc,xlim=c(0,1.2),ylim=c(45,210),xlab="Concentration",ylab="Rate",cex.lab=1.2)

### CHANGE BACKGROUND
par(bg="lightcyan")
plot(rate~conc,xlim=c(0,1.2),ylim=c(45,210),xlab="Concentration",ylab="Rate",cex.lab=1.2)

### ADD A REFERENCE LINE
### Let's add the regression line
reg<-lm(rate~conc)
abline(reg, lwd=2)


### CHANGE COLORS - Red for Treated, Black for Untreated.
### You can use numbers or you can use words, but for the latter, make sure you use " ".
names(Puromycin)
plot(rate~conc,xlim=c(0,1.2),ylim=c(45,210),xlab="Concentration",ylab="Rate",cex.lab=1.2,
     col=ifelse(state=="treated","red","black"),cex=c(2,2))


### CHANGE THE PLOTTING SYMBOL - pch(plottting character)
plot(rate~conc,xlim=c(0,1.2),ylim=c(45,210),xlab="Concentration",ylab="Rate",cex.lab=1.2,
     col=ifelse(state=="treated","green3","hotpink"),cex=c(1.5,1.5),pch=19)


### pch=21 empty circle, BG sets the inside, COL sets the border
plot(rate~conc,xlim=c(0,1.2),ylim=c(45,210),xlab="Concentration",ylab="Rate",cex.lab=1.2,
     bg=ifelse(state=="treated","royalblue","orangered"),
     cex=c(1.5,1.5),pch=21,col=c(1,1))

### ADD TEST INSIDE THE GRAPH
text(1.1, 152, label = "important point", pos = 1)

### CREATE TWO DATA SETS: Treated and Untreated
PuroT <- subset(Puromycin, state == "treated")
PuroU <- subset(Puromycin, state == "untreated")

### ADD SMOOTHING LINES
smooth <- with(PuroT, lowess(rate ~ conc))
lines(lowess(rate~conc), lty=1, lwd=2, col="royalblue")
smooth <- with(PuroU, lowess(rate ~ conc))
lines(smooth, lty=1, lwd=2, col="orangered")

### HORIZONTAL REFERENCE LINE
abline(h=200,lty=2)

### ADD TITLE AND LEGEND
title(main="Puromycin Data", cex.main=1.5)
legend(x=0.8, y=100, legend=c("Treated", "Untreated"), pch=c(19,19), col=c("royalblue","orangered"), lty=c(1,1), lwd=c(2,2), cex=c(1.2,1.2))


### REMOVE THE BOX AROUNND THE LEGEND -> bty="n"
legend("bottomright", legend=c("Treated", "Untreated"), pch=c(19,19), col=c("royalblue","orangered"),lty=c(1,1), lwd=c(2,2),cex=c(1.2,1.2), bty="n")


### CREATE MULTIPLE GRAPHS IN THE SAME WINDOW
par(mfrow=c(1,2))

### CHANGE THE MARGINS TO REMOVE EXTRA SPACE
#par(mar=c(4, 4, 0.5, 0.5))


### CHANGE THE OUTER MARGINS
#par(oma=c(0,0,3,0))
plot(rate~conc, data=PuroT, pch=21, bg="royalblue", col=1, xlab="Concentration", ylab="Rate", cex.lab=1.2)
plot(rate~conc, data=PuroU, pch=21, bg="orangered", col=1, xlab="Concentration", ylab="Rate", cex.lab=1.2)

### ADD A "COMMON" TITLE
mtext("Puromycin Data", side=3, adj=5, line=1.5, font=2, cex=2, col="red", outer=F)


### SAME THING USING XYPLOT()
# Separate scatterplots for each level of the factor
library(lattice)
xyplot(rate ~ conc | state, type = c("p", "smooth"), span=2, pch=19, col=2,
       main = "Puromycin", lwd=2, xlab="Concentration", ylab="Rate", cex.lab=1.2)


### Let's try par() wiht a regression object
reg<-lm(rate~conc)
par(mfrow=c(2,2))

### Change the margins of the plots
#par(mar=c(4, 4, 2, 1))
plot(reg)

############################################################################################################
######################         Scatterplot Matrix         ##################################################
############################################################################################################

plot(Puromycin)

### SAME THING WITH PAIRS()
pairs(Puromycin)

### ADD A SMOOTHING LINE
pairs(Puromycin, panel = panel.smooth,lwd=2)


############################################################################################################
####################         Multivariable Graph           #################################################
#################    Individual Profiles for 97 subjects    ################################################

### Prostate Data
data<-read.csv('F://PhD Program_MUSC//R Graphics//Prostate.csv',header=T)
dim(data)
data[1:10,]

### Standardize Predictors with scale() 
pred<-scale(data[,1:9],center=T,scale=T)

lcavol.st<-pred[,2]
lweight.st<-pred[,3]
age.st<-pred[,4]
lbhp.st<-pred[,5]
lcp.st<-pred[,7]

### DICHOTOMIZE PSA: N < 10 and H >= 10
psa<-exp(data[,10])
new.psa <- ifelse(psa >= 10, 1, 2)
new.data<-cbind(lcavol.st,lweight.st,age.st,lbhp.st,lcp.st,new.psa)

### CREATE TWO DATA SETS BY < 10 AND 10+ LEVELS OF PSA
new.dataN<-new.data[1:41,]
new.dataH<-new.data[42:97,]

### JITTER THE POINTS ON THE VERTICAL
n1<-ncol(new.dataN)-1
n2<-ncol(new.dataH)-1
noise1<-runif(n1,-.15,.15)  # BLUE
noise2<-runif(n2,-.15,.15)  # RED

### PLOT DATA BY PSA < 10 
plot(1:5,new.dataN[1,1:5] + noise1, type="b", pch=19, col="#0000FF32", cex=1.25, xaxt="n",
     xlab="", ylab="Standardized value", cex.lab=1.25, cex.axis=1.25, ylim=c(-3.1,2.7), lwd=2)

axis(side=1,at=c(1,2,3,4,5),labels=c("log CA vol","log weight","Age","log BHP","log CP"),cex.axis=1.25)

for (i in 2:41){
     lines(1:5, new.dataN[i,1:5]+ noise1, type="b", col="#0000FF32", cex=1.25, lwd=2, pch=19)
     }

### PLOT DATA BY THE PSA VALUES 10+
for (i in 1:56){
     lines(1:5, new.dataH[i,1:5]+noise2, type="b", col="#FF000032", cex=1.25, lwd=2, pch=19)
     }
legend("bottomright", legend=c("PSA < 10","PSA = 10+"), pch=19, col=c("#0000FF32","#FF000032"), lty=c(1,1), cex=1.25, bty="n", lwd=2)