Ggplot2

• Tutorials
  • https://wiki.nbic.nl/index.php/R_ggplot2_tutorial

• remove the grey background of all graphs: theme_set( theme_bw() )
• replot the last graph: last_plot() + modificationsYouWantToAdd

• Data
  • you can subset the dataframe, but then you need to do something like d$category = drop.levels(x, reorder=F, ...) (gdata package)