# Here is some code for using colors or symbols to represent populations in
# polysat.  Ten populations are assumed.  It is also assumed that you have
# done a Principal Coordinates Analysis and named it "pca" as in the
# "Getting Started" section of the tutorial manual.

## Using colors
# generate ten colors; there are other ways to do this, or you can make a character vector containing
# the color names that you want.  (Google "R colors")
popcolors <- rainbow(10)

# take a look at the colors generated
plot(1:10, 1:10, col=popcolors)

# for a plot containing all individuals
plot(pca[,1], pca[,2], col=popcolors[PopInfo(mydata)])

# for a plot containing a subset of individuals, called "subset" here
pca2 <- cmdscale(testmat[subset,subset])
plot(pca2[,1], pca2[,2], col=popcolors[PopInfo(mydata)[subset]])

## Using symbols
# Choose the first ten symbols in R; there are others.
popsym <- 0:9

# take a look at the symbols
plot(1:10, 1:10, pch=popsym)

# use the symbols in your plot
plot(pca[,1], pca[,2], pch=popsym[PopInfo(mydata)])

## Using a combination of colors and symbols
popsym <- c(0,0,1,1,2,2,5,5,6,6)
popcol <- rep(c("red","blue"), times=5)
plot(1:10, 1:10, pch=popsym, col=popcol)
plot(pca[,1], pca[,2], pch=popsym[PopInfo(mydata)], col=popcol[PopInfo(mydata)])