bin_pv_distribution: bin_pv_distribution

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

Usage

bin_pv_distribution(alloutputs, lowindx, folder, pvtitle, pvpicdim)

Arguments

alloutputs
lowindx
folder
pvtitle
pvpicdim

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, lowindx, folder, pvtitle, pvpicdim) 
{
    dir.create(path = folder, showWarnings = FALSE)
    df <- alloutputs$alldist$pvdist
    df <- data.frame(df)
    df$pvalue <- 10^(-as.numeric(as.character((df[, "rep"]))))
    library(ggplot2)
    for (i in 0:lowindx) {
        p <- ggplot(df[df$dif == i, ], aes(x = pvalue)) + xlim(0, 
            1) + geom_histogram(aes(fill = ..count..), color = "black", 
            bins = 21, position = "dodge", boundary = 0)
        if (i == 0) {
            temp <- ggplot_build(p)$data[1]
        }
        p + geom_vline(aes(xintercept = 0.05), color = "#ff00cc", 
            linetype = "dashed", size = 2, show.legend = F) + 
            ylim(c(0, 1.1 * (max(temp[[1]]$y)))) + ggtitle(paste(pvtitle, 
            "permutation proportion", round(i/lowindx, 2), sep = " ")) + 
            theme_bw() + theme(plot.title = element_text(hjust = 0.5, 
            size = 30), legend.title = element_text(size = 20), 
            legend.text = element_text(size = 12)) + theme(panel.background = element_blank(), 
            axis.text = element_text(size = 24, face = "bold"), 
            axis.title = element_text(size = 20, face = "bold"), 
            panel.border = element_rect(colour = "black", fill = NA, 
                size = 0.5))
        ggsave(filename = paste(folder, "/", round(i/lowindx, 
            2), "_permute", "_pvalue.eps", sep = ""), width = 7, 
            height = 7)
    }
  }

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