expanded features of manhattan()

1. Optional color and size specification of points
(pt.col=c('gray10','gray50'), pt.bg=c('gray10','gray50'), pt.cex=0.4)

2. Optional gridlines
(gridlines=T, gridlines.col='gray83')

3. Option to make ymax soft (description below)
(ymax=8, ymax.soft=T)
# If ymax.soft==T, the specified value of ymax is the lower bound of ymax [i.e., if the data contains a larger value, then ymax=max(data)]. If ymax.soft==F, the specified value of ymax is absolute/hard.

4. Optional color and lwd specification of significance lines
(suggestiveline.col='blue',suggestiveline.lwd=1.5)

5. Optional highlight color selection (including different colors for different regions)
(highlight.col=c('green3','magenta'),highlight.bg=c('green3','magenta))

6. Optional annotation of top snps
(annotate=c('rs13895','rs20762'), annotate.font=3, annotate.cex=0.7)