# Annotating a plot
# R Graphics seminar
# 11 February 2013
#NJG

####################################################
#  Standard calls for preserving defaults, and reading a csv
opar <- par(no.readonly=TRUE)
Ant.Data <- read.csv("antcountydata.csv",header=TRUE)
attach(Ant.Data)

plot(lat.centroid,n.species,log="y") # log transforms; use x,y, or xy
plot(lat.centroid,n.species)
abline(h=20) # drawing a horizontal line
abline(v=46,lwd=2,lty="twodash",col="grey") # drawing a vertical line
abline(a=-1600,b=40) # intercept and slope
abline(lm(n.species~lat.centroid)) # standard regression
lines(lowess(n.species~lat.centroid),col="blue",lty="dotdash",lwd=1.5)
rug(lat.centroid) # show the density of data points
rug(n.species,side=2) # can be done on any axis for any variable
grid()
box(which="outer") # box options: outer, inner, figure, plot
box(col="gray",lwd=5)
text(44,60,"my text here at 44,60")
# cleaned up regression
par(mar=c(4,6,2,2)+0.1)
plot(lat.centroid,n.species,
     xlab="Latitude",ylab="Number of Species",
     las=1,cex.axis=1.2,cex.lab=1.5)
reg.model <- lm(n.species~lat.centroid)
abline(reg.model)
rug(n.species,side=2)
grid()
# text annotations

x <- 1:5
y <- seq(1,5,1)
plot(x,y)
text(1,1,"right",pos=4) # use pos to offset the text
# use vectors for multiple plotting
plot(x,y,ann=FALSE, axes= FALSE, col="blue")
box(col="gray")
text(x[-3],y[-3],c("right","top","bottom","left"),pos=c(4,3,1,2))
text(3,3,"overlay")
text(4,2,"angle = 10 degrees",srt=10)

# illustration of plot math
plot(x,y,ann=FALSE, axes= FALSE, type="n")
box(col="gray")

text(3,4,
     expression(sqrt(x[i]^2+y[i]^2)-hat(beta)))

text(3,3,
     expression(bar(x) == sum(frac(x[i], n),
                              i == 1,n)))


# text(3,3,
#      expression(bar(x) == sum(frac(x[i], n),
#                 i == 1,n)),
#      cex=4,col="red",font=1,srt=-10)

text(3,2,
     expression(paste("Temperature (", degree,
                      "C) in 2013")))
detach(Ant.Data) # detach ant data
par(opar) # restore original parameters
ls() # list objects in memory
rm(list=ls()) # remove all objects from memory - optional!