n <- 80
set.seed(32611)
x <- sort(runif(n, min = 0, max=2*pi))
y <- sin(x) + rnorm(n, mean = 0, sd = 0.2)
plot(x,y)

plot(x,y, type="p") ## default is "p"

plot(x,y, type="l") ## # default xlab and ylab are the variable

plot(x,y, type="b")

plot(x,y, type="o")

plot(x,y, type="n")

plot(x,y, main="sin function with Gaussian noise", 
     xlab="x axis", ylab="y axis") 

plot(x,y, main="sin function with Gaussian noise", 
     xlab="x axis", ylab="y axis", 
     cex=2, cex.axis=2, cex.lab=2, cex.main=2, cex.sub=2) 

letters[1:10] ## letters contain a-z

plot(x=1:10, y=1:10, type="n", main = "some texts") 
text(x = 1:10, y=1:10, labels = letters[1:10])

letters[1:10] ## letters contain a-z

plot(x=1:10, y=1:10, main = "some texts") 
text(x = 1:10, y=1:10, labels = letters[1:10], pos = NULL)

plot(1:10, type="n", xlab="X", ylab="Y")
text(5.5, 9, "expression(y==alpha[1]*x+alpha[2]*x^2)", cex=1.5)
text(5.5, 8, expression(y==alpha[1]*x+alpha[2]*x^2), cex=1.5)
theta = 3
text(5.5, 6, "bquote(hat(theta)==.(theta))", cex=1.5)
text(5.5, 5, bquote(hat(theta)==.(theta)), cex=1.5)

plot(1:25,1:25,pch=1:25)

plot(x,y, pch=19) 

n <- 80
set.seed(32611)
x <- sort(runif(n, min = 0, max=2*pi))
y1 <- sin(x) + rnorm(n, mean = 0, sd = 0.2)
y2 <- cos(x) + rnorm(n, mean = 0, sd = 0.2)

par(mfrow=c(1,2))
plot(x,y1, main="sin plot")
plot(x,y2, main="cos plot")

par(mfrow=c(2,2))
plot(x,y, type="l",lwd=1) 
plot(x,y, type="l",lwd=2) 
plot(x,y, type="l",lwd=3) 
plot(x,y, type="l",lwd=4) 

plot(0:6, 0:6, type = "n")
abline(a = 3, b = -1)

plot(0:6, 0:6, type = "n")
abline(h = 3)
abline(v = 3, col=2)

z <- lm(dist ~ speed, data = cars)
plot(cars)
abline(z) # equivalent to abline(reg = z) or

# abline(coef = coef(z))

plot(1:8,1:8, col=1:8) 

par(mfrow=c(2,2))
plot(x,y, main = "black color") ## default is black
plot(x,y, main = "blue color", col=4) ## basic color option 1:8
plot(x,y, main = "green color", col='green') ## find colors from colors()
plot(x,y, main = "red color", col='#FF0000') ## RGB mode

n <- 10
par(mfrow=c(2,3))
plot(1:n,1:n, col=rainbow(n), main = "rainbow") 
plot(1:n,1:n, col=heat.colors(n), main = "heat.colors") 
plot(1:n,1:n, col=terrain.colors(n), main = "terrain.colors") 
plot(1:n,1:n, col=topo.colors(n), main = "topo.colors") 
plot(1:n,1:n, col=cm.colors(n), main = "cm.colors") 

curve(sin, from = 0, to = 2*pi)

chippy <- function(x) sin(cos(x)*exp(-x/2))
curve(chippy, -8, 7, n = 2001) # n specify number of points used to draw the curve, default n = 101

curve(sin, 0, 2*pi, col=2)
curve(cos, 0, 2*pi, col=4, add=T) ## add=T to overlay a new curve on top of the original figure
legend("bottomleft", legend = c("sin", "cos"), col = c(2,4),lty = 1)

plot(1:3,1:3,col = "blue")
segments(x0 = 3,y0 = 3,x1 = 1,y1 = 1,lwd=2,col=2)

plot(1:3,1:3,col = "blue")
arrows(x0 = 3,y0 = 3,x1 = 1,y1 = 1,code=1,angle=30,length=.1,lwd=2)

plot(1:3,1:3,col = "blue")
polygon(x = c(2,3,3,2),y = c(2,2,3,3),col="pink")

set.seed(32611)
curve(dnorm,-4,4, ylim = c(-0.1, 0.5)) 

# shaded area
xvals <- seq(-4,2,length=100) 
dvals <- dnorm(xvals)
polygon(c(xvals,rev(xvals)),c(rep(0,100),rev(dvals)),col="gray")

#label pnorm as area under the curve 
arrows(1,.15,2,.25,code=1,angle=30,length=.1,lwd=2)
text(2,.25,paste('pnorm(2) =',round(pnorm(2),3)),cex=.75,pos=3)

#label dnorm as height
segments(2,0,2,dnorm(2),lwd=2,col=2)
arrows(2,.025,2.5,.1, code=1, angle=30, length=.1, lwd=2, col=2)
text(2.5,.1,paste('dnorm(2) =', round(dnorm(2),3)), cex=.75, pos=3, col=2)

#label qnorm as quantile
points(2,0,col=4,pch=16,cex=1.1)
arrows(2,0,3,.05,code=1,angle=30,length=.1,lwd=2,col=4)
text(3,.05,paste('qnorm(',round(pnorm(2),3),') = 2'), cex=.75,pos=3,col=4)

mtext(side=3,line=.5,'X ~ Normal(0,1)',cex=.9,font=2)
points(rnorm(20),jitter(rep(0,20)),pch=18,cex=.9)
legend(-4,.3,'rnorm(20)',pch=18,cex=.8,bty='n')

par(mar=c(1,2,3,4)) # bottem, left, top, right order, inner margin
plot(x, y, main="Red sin", pch=20, col="red")

par(oma = c(4,3,2,1), mar=c(1,2,3,4)) # bottem, left, top, right order, inner margin and outer margin
plot(x, y, main="Red sin", pch=20, col="red")

plot(1:10, type="n", xlab="X", ylab="Y")
mtext(text = "mtext", side = 4, line = 1, col="red")

n <- 80
set.seed(32611)
x <- sort(runif(n, min = 0, max=2*pi))
y <- sin(x) + rnorm(n, mean = 0, sd = 0.2)

pdf("sinFunction.pdf")
plot(x,y)
dev.off()

data(iris)
head(iris)

str(iris)

boxplot(Petal.Length ~ Species, data = iris)

names(iris)

par(mfrow = c(2,2))
for(i in 1:4){
  aname <- names(iris)[i]
  boxplot(iris[[i]] ~ iris$Species, xlab="Species", col=i, ylab=aname, main=aname)  
}

par(mfrow=c(2,2))
hist(iris$Petal.Length) ## default
hist(iris$Petal.Length, nclass=50) ## set number of bins
hist(iris$Petal.Length,  prob=TRUE, col="grey") ## grey color
lines(density(iris$Petal.Length), col="blue") ## and put the density function on top of the histogram

par(mfrow = c(2,2))
xlims <- range(iris$Petal.Length) ## set common x limits
uniqueSpecies <- levels(iris$Species)
for(i in seq_along(uniqueSpecies)){
  aspecies <- uniqueSpecies[i]
  sampleSelection <- iris$Species==aspecies
  adata <- iris$Petal.Length[sampleSelection]
  hist(adata, col=i, xlim=xlims, xlab="petal length",main=aspecies)
}

x <- y <- seq(-1, 1, len=25)
z <- outer(x, y, FUN=function(x,y) -x*y*exp(-x^2-y^2))
# Contour plots
contour(x,y,z, main="Contour Plot")

filled.contour(x,y,z, main="Filled Contour Plot")

filled.contour(x,y,z, color.palette = heat.colors)

filled.contour(x,y,z, color.palette = colorRampPalette(c("red", "white", "blue")))

matrix <- as.matrix(iris[,1:4])
image(matrix)

heatmap(matrix)

heatmap(matrix, Rowv = NA, Colv = NA)

B=16
greenRed <- rgb(c(rep(0, B), (0:B)/B), c((B:0)/16, rep(0, B)), rep(0, 2*B+1))
heatmap(matrix, col= greenRed, Rowv = NA, Colv = NA)

B=16
greenRed <- rgb(c(rep(0, B), (0:B)/B), c((B:0)/16, rep(0, B)), rep(0, 2*B+1))

species <- iris$Species
levels(species) <- 1:3
rowColor <- palette()[species]

heatmap(matrix, col= greenRed, 
        Rowv = NA, Colv = NA, RowSideColors = rowColor)

B=16
greenRed <- rgb(c(rep(0, B), (0:B)/B), c((B:0)/16, rep(0, B)), rep(0, 2*B+1))

species <- iris$Species
levels(species) <- 1:3
rowColor <- palette()[species]

heatmap(matrix, col= greenRed, margin=c(7,7), 
        Rowv = NA, Colv = NA, RowSideColors = rowColor)
legend("topright",legend = levels(iris$Species),fill=levels(species))

B=16
greenRed <- rgb(c(rep(0, B), (0:B)/B), c((B:0)/16, rep(0, B)), rep(0, 2*B+1))

species <- iris$Species
levels(species) <- 1:3
rowColor <- palette()[species]

heatmap(matrix, col= greenRed,  margin=c(7,7), 
        Rowv = NA, Colv = NA, 
        RowSideColors = rowColor, 
        labRow = "", labCol = "", main="heatmap of iris data")
legend("topright",legend = levels(iris$Species),fill=levels(species))