#read the table and create a screen to plot 
#divided in 2*2 spaces

# here's how to read in the data under Unix
fish_read.table("fish.asc",header=T)
motif()
par(mfrow=c(2,2))

# first two histograms
hist(fish$conc,xlab="Concentration ppm",
ylab="Count",main="Mercury\nconcentrations")
fish$logconc_log(fish$conc,base=10)
hist(fish$logconc,xlab="log concentration ppm",
ylab="Count",main="Log Mercury concentrations")

# boxplots
# split the boxplot to have two in the same graph
# use split(vble,vble) into the boxplot command
boxplot(split(fish$logconc,fish$river),
ylab="log concentration ppm",xlab="river",
main="concentration by river")
boxplot(split(fish$logconc,fish$station),
ylab="log concentration ppm",xlab="station",
main="Concentration by station")

# length and width with identification of outliers
plot(fish$length,fish$weight,xlab="length in cm",
ylab="length in gm",main="Fish size",pch=1)
# click on the graph to put an identification 
# number to the data. Don't forget to click the
# middle button of your mouse to quit.
identify(fish$length,fish$weight,fish$station)

# plot of length and weight using station number as 
# plotting symbol
plot(fish$length,fish$weight,xlab="length in cm",pch=1,
type="n",ylab="length in gm",main="fish size by station")
# Make the symbols .7 times as their regular size using 
# cex in the text command.
text(fish$length,fish$weight,fish$station,cex=.7)
plot(fish$weight,fish$logconc,xlab="weight in gm",
ylab="log concentration ppm",pch=1,
main="Log concentration by weight")

# If you'd rather use a different plotting symbol,
# here's a way to do that.
plot(fish$length,fish$weight,xlab="length in cm",pch=1,
type="n",ylab="length in gm",main="fish size by station")
for(i in 1:16) points(fish$length[fish$station==i],
  fish$weight[fish$station==i],pch=i)

# if you want to see what plotting symbols are available
# here's a way to do it:
plot(c(0,21),c(0,3),type="n")
for(i in 1:20){
  points(i,1,pch=i)
  text(i,2,i)
}
text(10,2.3,"pch number",cex=1.2)
text(10,1.3,"plotting symbol",cex=1.2)

# Weight by logconc.  I'll use different plotting symbols
# and a legend
rivernum_ifelse(fish$river=="wacamaw",1,2)
plot(fish$weight,fish$logconc,xlab="length in cm",pch=1,
type="n",ylab="log concentration (ppm)",main="weight by mercury conc")
for(i in 1:2) points(fish$weight[rivernum==i],
  fish$logconc[rivernum==i],pch=i)
legend(2800,-0.6,legend=c("Wacamaw R","Lumber R"),marks=c(1,2),cex=.8)
# the first two entries give the x,y coordintates of the 
# upper-left of the legend box; for more info type: ?legend

# Now, length by logconc
plot(fish$length,fish$logconc,xlab="length in cm",pch=1,
type="n",ylab="log concentration (ppm)",main="length by mercury conc")
for(i in 1:2) points(fish$length[rivernum==i],
  fish$logconc[rivernum==i],pch=i)
legend(48,-0.6,legend=c("Wacamaw R","Lumber R"),marks=c(1,2),cex=.8)


par(mfrow=c(1,1))
# take columns 3,4 and 6 (logconc) and graph them together
pairs(fish[,c(3,4,6)])
# That's it.