plot_con_permute_sigcurve: plot_con_permute_sigcurve

In LyonsZhang/ProgPermute: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries

Usage

plot_con_permute_sigcurve(alloutputs, samsize, lgndcol = 2, psigtitle, savepsigfile, psigpicdim)

Arguments

alloutputs
samsize
lgndcol
psigtitle
savepsigfile
psigpicdim

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (alloutputs, samsize, lgndcol = 2, psigtitle, savepsigfile, 
    psigpicdim) 
{
    require(ggplot2)
    results <- alloutputs$alldist
    selname0 <- alloutputs$selname
    df <- as.data.frame(results$psigdist)
    df$highlight <- ifelse(df$dif == 0, "real data", "permutation")
    df$highlight <- factor(df$highlight, levels = c("real data", 
        "permutation"))
    df$prop <- df$median/samsize
    mycolours <- c(permutation = "black", `real data` = "red")
    N0 <- max(df$dif)
    if (sum(is.na(df))) {
        stop("Missing values exist in psigdist")
    }
    else {
        df$dif <- df$dif/N0
        auc <- DescTools::AUC(df$dif, df$prop, method = "trapezoid", 
            na.rm = FALSE)
        aoi <- mean(df$prop[c(1, length(df$prop))])
        slope <- diff(df$prop)/diff(df$dif)
        ggplot(df, aes(x = dif, y = prop)) + geom_point(size = 5, 
            aes(colour = highlight)) + scale_color_manual("Scenarios", 
            values = mycolours) + geom_pointrange(aes(ymin = q1/samsize, 
            ymax = q2/samsize, colour = highlight), size = 0.5) + 
            geom_line(size = 1) + geom_ribbon(aes(ymin = 0, ymax = prop), 
            alpha = 0.2, fill = "purple") + geom_ribbon(aes(ymin = prop, 
            ymax = prop[1]), alpha = 0.2, fill = "green") + geom_ribbon(aes(ymin = prop[1], 
            ymax = 1), alpha = 0.2, fill = "gold") + xlab("Proportion of exchanges") + 
            ylab("Proportion of significant features") + ggtitle(psigtitle) + 
            ylim(c(0, 1)) + annotate("text", x = 0.5, y = 0.9, 
            label = paste("aoi=", round(aoi, 3)), size = 6, colour = "green") + 
            annotate("text", x = 0.5, y = 0.8, label = paste("auc=", 
                round(auc, 3)), size = 6, colour = "purple") + 
            annotate("text", x = 0.5, y = 0.7, label = paste("slope=", 
                round(slope[1], 3)), size = 6, colour = "red") + 
            theme_bw() + theme(plot.title = element_text(size = 30, 
            face = "bold"), legend.title = element_text(size = 20), 
            legend.text = element_text(size = 16)) + theme(axis.line = element_line(colour = "black"), 
            panel.grid.major = element_blank(), panel.border = element_blank(), 
            panel.background = element_blank(), axis.line.x = element_line(color = "black", 
                size = 1.5), axis.line.y = element_line(color = "black", 
                size = 1.5), axis.text = element_text(size = 16, 
                face = "bold"), axis.title = element_text(size = 20, 
                face = "bold"))
        ggsave(filename = savepsigfile, width = psigpicdim[1], 
            height = psigpicdim[2], device = cairo_ps)
        return(list(auc = auc, aoi = aoi, slope = slope, df = df))
    }
  }

LyonsZhang/ProgPermute documentation built on July 22, 2020, 4:09 p.m.