peptideBarPlot: working on...

In PengyiYang/ReFraction: A machine learning approach for deterministic identification of protein homologues and splice variants in large-scale MS-based proteomics

Usage

peptideBarPlot(peptide.assignment.fraction, peptide.assignment.original, prefix)

Arguments

peptide.assignment.fraction
peptide.assignment.original
prefix

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 (peptide.assignment.fraction, peptide.assignment.original, 
    prefix) 
{
    peptide.slice.unique.idx <- lapply(strsplit(peptide.assignment.fraction, 
        ";"), length) == 1
    peptide.original.unique.idx <- lapply(strsplit(peptide.assignment.original, 
        ";"), length) == 1
    unique.count <- matrix(nrow = 2, ncol = 2)
    unique.count[1, 1] <- sum(peptide.original.unique.idx)
    unique.count[1, 2] <- sum(peptide.slice.unique.idx)
    unique.count[2, 1] <- length(peptide.original.unique.idx) - 
        sum(peptide.original.unique.idx)
    unique.count[2, 2] <- length(peptide.slice.unique.idx) - 
        sum(peptide.slice.unique.idx)
    dev.new(width = 3.5, height = 5)
    barplot(unique.count, ylim = c(0, 20000), ylab = "Number of Peptides", 
        names = c("Original", "Re-Fraction"), col = c("darkblue", 
            "red"), legend = c("Unique Peptide", "Shared Peptide"), 
        horiz = F, border = NA)
    text(0.7, unique.count[1, 1]/2, unique.count[1, 1], cex = 1, 
        col = "white")
    text(0.7, unique.count[1, 1] + unique.count[2, 1]/2, unique.count[2, 
        1], cex = 1, col = "white")
    text(1.9, unique.count[1, 2]/2, unique.count[1, 2], cex = 1, 
        col = "white")
    text(1.9, unique.count[1, 2] + unique.count[2, 2]/2, unique.count[2, 
        2], cex = 1, col = "white")
    dev.new(width = 3.5, height = 5)
    peptide.assignment.ratio <- c(sum(peptide.original.unique.idx)/length(peptide.original.unique.idx), 
        sum(peptide.slice.unique.idx)/length(peptide.slice.unique.idx))
    peptide.assignment.ratio <- round(peptide.assignment.ratio * 
        100)
    barplot(peptide.assignment.ratio, names = c("Original", "Re-Fraction"), 
        ylab = "Percentage of Unique Peptide (%)", col = c("darkblue", 
            "red"), border = NA)
    text(0.7, peptide.assignment.ratio[1]/2, paste(round(peptide.assignment.ratio[1]), 
        "%", sep = ""), cex = 1, col = "white")
    text(1.9, peptide.assignment.ratio[2]/2, paste(round(peptide.assignment.ratio[2]), 
        "%", sep = ""), cex = 1, col = "white")
  }

PengyiYang/ReFraction documentation built on May 14, 2019, 11:01 p.m.