# R in Action (2nd ed): Chapter 3
# Getting started with graphs
# requires that the Hmisc package has been installed
# install.packages("Hmisc")
#-----------------------------------------------------

par(ask=TRUE)
opar <- par(no.readonly=TRUE) # make a copy of current settings

attach(mtcars) # be sure to execute this line

plot(wt, mpg)
abline(lm(mpg~wt))
title("Regression of MPG on Weight")


# Input data for drug example
dose  <- c(20, 30, 40, 45, 60)
drugA <- c(16, 20, 27, 40, 60)
drugB <- c(15, 18, 25, 31, 40)

plot(dose, drugA, type="b")

par(lty=2, pch=17)          # change line type and symbol
plot(dose, drugA, type="b") # generate a plot
par(opar)                   # restore the original settings 

plot(dose, drugA, type="b", lty=3, lwd=3, pch=15, cex=2)

n <- 10
mycolors <- rainbow(n)
pie(rep(1,n), labels=mycolors, col=mycolors)

# Using graphical parameters to control graph appearance	
par(pin=c(2,3))					
par(lwd=2, cex=1.5)							
par(	cex.axis=.75, font.axis=3)						
plot(dose, drugA, type="b", pch=19, lty=2, col="red")
plot(dose, drugB, type="b", pch=23, lty=6, col="blue", bg="green")	
par(opar)				


plot(dose, drugA, type="b",  
     col="red", lty=2, pch=2, lwd=2,
     main="Clinical Trials for Drug A", 
     sub="This is hypothetical data", 
     xlab="Dosage", ylab="Drug Response",
     xlim=c(0, 60), ylim=c(0, 70))


# An Example of Custom Axes
x <- c(1:10)
y <- x
z <- 10/x
par(mar=c(5, 4, 4, 8) + 0.1)
plot(x, y,type="b",
     pch=21, col="red", 
     yaxt="n", lty=3, xlab="", ylab="")
lines(x, z, type="b", 
      pch=22, col="blue", lty=2) 
axis(2, at=x,labels=x, col.axis="red", las=0) 
axis(4, at=z,labels=round(z,digits=2),
     col.axis="blue", las=2, cex.axis=0.7, tck=-.01) 
mtext("y=10/x", side=4, line=3, cex.lab=1,las=2, col="blue") 
title("An Example of Creative Axes", 
      xlab="X values",
      ylab="Y=X")
par(opar)

# Comparing Drug A and Drug B response by dose
par(lwd=2, cex=1.5, font.lab=2)
plot(dose, drugA, type="b", 
     pch=15, lty=1, col="red", ylim=c(0, 60),
     main="Drug A vs. Drug B",
     xlab="Drug Dosage", ylab="Drug Response")
lines(dose, drugB, type="b", 
      pch=17, lty=2, col="blue")
abline(h=c(30), lwd=1.5, lty=2, col="grey")
library(Hmisc)
minor.tick(nx=3, ny=3, tick.ratio=0.5)		
legend("topleft", inset=.05, title="Drug Type", c("A","B"), 
       lty=c(1,2), pch=c(15, 17), col=c("red", "blue"))
par(opar)


# Example of labeling points
plot(wt, mpg, 
     main="Milage vs. Car Weight", 
     xlab="Weight", ylab="Mileage", 
     pch=18, col="blue")
text(wt, mpg, 
     row.names(mtcars), 
     cex=0.6, pos=4, col="red")

# View font families 
par(cex=1.5)
plot(1:7,1:7,type="n")
text(3,3,"Example of default text")
text(4,4,family="mono","Example of mono-spaced text")
text(5,5,family="serif","Example of serif text")
par(opar)


# combining graphs
par(mfrow=c(2,2))
plot(wt,mpg, main="Scatterplot of wt vs. mpg")
plot(wt,disp, main="Scatterplot of wt vs disp")
hist(wt, main="Histogram of wt")
boxplot(wt, main="Boxplot of wt")
par(opar)

par(mfrow=c(3,1)) 
hist(wt)
hist(mpg)
hist(disp)
par(opar)

layout(matrix(c(1,1,2,3), 2, 2, byrow = TRUE))
hist(wt)
hist(mpg)
hist(disp)


layout(matrix(c(1,1,2,3), 2, 2, byrow = TRUE), 
       widths=c(3,1), heights=c(1,2))
hist(wt)
hist(mpg)
hist(disp)


par(fig=c(0,0.8,0,0.8))
plot(mtcars$wt, mtcars$mpg, 
     xlab="Miles Per Gallon", 
     ylab="Car Weight")
par(fig=c(0,0.8,0.55,1), new=TRUE)
boxplot(mtcars$wt, horizontal=TRUE, axes=FALSE)
par(fig=c(0.65,1,0,0.8),new=TRUE)
boxplot(mtcars$mpg, axes=FALSE)
mtext("Enhanced Scatterplot", side=3, outer=TRUE, line=-3)
par(opar)