# helper functions
plot_sig <- function(sigtab, x="Species", color="Species", rank1="Family", rank2="Species", alpha=0.05, title=""){
	sig = sigtab[which(sigtab$padj < alpha), ]
	y = tapply(sig$log2FoldChange, sig[, rank1], function(z) max(z))
	y = sort(y, TRUE)
	sig[, rank1] = factor(as.character(sig[, rank1]), levels=names(y))
	y = tapply(sig$log2FoldChange, sig[, rank2], function(z) max(z))
	y = sort(y, TRUE)
	sig[, rank2] = factor(as.character(sig[, rank2]), levels=names(y))
	return(ggplot(sig, aes_string(x=x, y="log2FoldChange", color=color)) +
  	geom_point(aes(size=baseMean)) + guides(col = guide_legend(ncol = 1)) +
  	theme(axis.text.x = element_text(angle = 90, vjust=0.5)) + ggtitle(title))
}
plot_volcano <- function(sigtab, color="Family", label="Species", title=""){
  our_copy <- sigtab
  our_copy[,"neg.log10.padj"] <- -log10(our_copy$padj)
  return(ggplot(our_copy, aes_string(x="log2FoldChange", y="neg.log10.padj", color=color, label=label)) +
  geom_point(size=3)  + geom_label() +
  theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5), legend.position="bottom") +
  ggtitle(title) + geom_hline(aes(yintercept=-log10(.05))) + geom_vline(aes(xintercept=1)) + geom_vline(aes(xintercept=-1)))

}