R/plot.mGST.R

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

plot.mGST <-
function (x, gene_sets = NULL, order_by = "logit2NES", top = 30, 
    eps = 0.25, as.network = FALSE, similarity_threshold = 1/3, 
    manipulation = FALSE, autoResize = TRUE, ...) 
{
    if (as.network) {
        if (is.null(gene_sets)) 
            stop("The gene-sets collection is not provided.")
        ans <- plot_network(x, gene_sets, eps = eps, similarity_threshold = similarity_threshold, 
            manipulation = manipulation, autoResize = autoResize, 
            ...)
        return(ans)
    }
    x <- summary(x, top = top, order_by = order_by)
    x$signed_NES <- 2 * (x$NES - 0.5)
    bbreaks <- seq(from = -1, to = 1, length.out = 100)
    ccolors <- colorRampPalette(c("green2", "white", "red2"))(99)
    x$NES.col <- cut(x$signed_NES, breaks = bbreaks, include.lowest = TRUE)
    levels(x$NES.col) <- ccolors
    x$NES.col <- as.character(x$NES.col)
    x$rowname <- rownames(x)
    x$rowname <- paste0(x$rowname, " (", round(x$logit2NES, 2), 
        ")")
    x <- x[rev(rownames(x)), ]
    howMany <- nrow(x)
    bar_width <- 1/howMany
    spacing <- 1/(5 * howMany)
    from <- cumsum(c(0, rep(bar_width + spacing, howMany)))
    mmax <- max(from)
    from <- (from/mmax)[-(howMany + 1)]
    to <- from + bar_width/mmax
    plot(c(-1, 1), c(1, 0), col = "white", main = "Enrichment plot", 
        xlab = "signed NES (logit2NES in parentesis)", ylab = "", 
        yaxt = "n", bty = "n")
    rect(0, from, x$signed_NES, to, col = as.character(x$NES.col), 
        border = NA)
    text(0, (from + to)/2, x$rowname, adj = 0.5)
    invisible(NULL)
}