Expanded features of qq()

1. Optional color specification of the points and abline.
(pt.col='black', pt.bg='black', abline.col='red')

2. Optional grid lines.
(grid=TRUE, grid.col='gray88')

3. Optional 95% confidence intervals.
(confidence=TRUE, confidence.col='gray76')

4. Optional highlighting of data points of interest.
(highlight=c('rs20762','rs13895','rs11846'), highlight.col = 'blue', highlight.bg = 'blue')

5. Optional annotation (rs_id) of data points of interest.
Simplified argument checking in qq().
qq: sped up approximation of confidence intervals
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)
Fixed bug where missing CHR data causes error

Also added staggered chr labels in manhattan()
modified qq() to take pvect instead of dataframe
Merge pull request #2 from stephenturner/dev

Dev