Improve plot appearance

Plot issues
# default line widths/colours now match PL's
# black and magenta colours now explained on the key
# point colours changed to pleasant alternatives
# point colours added to species key
# point colours and sizes added to object key
# point and line keys vertically arranged
# switch line colours to RColorBrewer palette
# use switch() for setting key options, rather than if()
# set window arrangement and main.plot with different functions, both
called by a wrapper function plot.pairs()

Other Stuff:
# remove verbose output from pairwise.odds.ratios
# help now available for plot.pairs()