R/plot.mORT.R

In massiveGST: Competitive Gene Sets Test with the Mann-Whitney-Wilcoxon Test

plot.mORT <-
function (x, gene_sets = NULL, order_by = "log2_odds_ratio", 
    top = 30, eps = 0.25, as.network = FALSE, similarity_threshold = 1/3, 
    manipulation = FALSE, autoResize = TRUE, ...) 
{
    x$NES <- pnorm(x$log2_odds_ratio)
    x$logit2NES <- x$log2_odds_ratio
    x$actualSize <- x$geneSet_size
    alternative <- attr(x, "alternative")
    if (alternative == "two.sided") 
        x$abs_logit2NES <- abs(x$logit2NES)
    if (order_by == "log2_odds_ratio") 
        order_by = "logit2NES"
    if (order_by == "odds_ratio") 
        order_by = "NES"
    class(x)[1] <- "mGST"
    plot(x, gene_sets = gene_sets, order_by = order_by, top = top, 
        eps = eps, as.network = as.network, similarity_threshold = similarity_threshold, 
        manipulation = manipulation, autoResize = autoResize, 
        ...)
}