I am plotting all sites based on p-value and would like to do two things:

1. Remove everything that aligns as a straight line at 1.

2. Pseudocolor points on the plot that have a high adjusted p-value score a different color.

Thanks.

I'm not sure what you mean in your first point, but the options for dba.plotVolcano() are fairly limited.

You can call dba.report() to get all the data used in the plot to make your own more detailed plots. The axes labels in show exactly what is being plotted.

Cheers-

Rory