graph_genescf_output.R

#requires tab delimited output file after running genescf
#re-generates default scatterplot output from genescf with improved readability 
#requires two arguments from r console: imported raw genescf output table and name of sample group

graph_genescf <- function(table, name){
  require(ggplot2)
  require(plyr)
  table <- table[,c(2,3,4,5,6)] 
  table <- arrange(table, P.value)
  table <- table[1:20,]
  table$rank_position <- 1:20
  g <- ggplot(table, aes(x = rank_position, y = -log10(P.value)))   + geom_point(aes(color = reorder(Process.name, rank_position)), show.legend = T) + theme(legend.text = element_text(size = 6))  + geom_hline(yintercept = -log10(0.05)) + labs(color = "Top 20 Ranked Processes") + labs(title = "Top Enriched GO:BP terms", subtitle = name) + xlab("Ranked Position")
  return(g)
}

g