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| # 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)) + |