R/boxPlot.R

In statTarget: Statistical Analysis of Molecular Profiles

### Box Plot Box Plot of each metabolite between groups.  file The connection for intensity of
### metabolites in each group.  The box plot
boxPlot <- function(file) {
    pwdfile = paste(getwd(), "/Univariate/DataTable.csv", sep = "")
    file = pwdfile
    x <- read.csv(file, sep = ",", header = TRUE)
    x.x = x[, 3:ncol(x)]
    rownames(x.x) = x[, 2]
    k = matrix(x[, 1], ncol = 1)
    slink = paste(getwd(), "/DataPretreatment", "/slink.csv", sep = "")
    slink = read.csv(slink, header = TRUE)
    colnames(k)[1] = "Class"
    x.x = cbind(k, x.x)
    sorted = x.x[order(x.x[, 1]), ]
    sorted.x = as.matrix(sorted[, -1], ncol = ncol(sorted) - 1)
    g = c()
    for (i in 1:nrow(sorted)) {
        if (any(g == sorted[i, 1])) {
            g = g
        } else {
            g = matrix(c(g, sorted[i, 1]), ncol = 1)
        }
    }
    NoF = nrow(g)
    dirbox = paste(getwd(), "/Univariate/BoxPlot/", sep = "")
    dir.create(dirbox)
    for (i in 2:ncol(x.x)) {
        name = paste(getwd(), "/Univariate/BoxPlot/", colnames(x.x)[i], ".pdf", sep = "")
        pdf(name)
        boxplot(x.x[, i] ~ slink[, 1], boxfill = c(seq(1, NoF, 1)), ylab = colnames(x.x)[i], xlab = "Groups", 
            border = "grey30", main = paste("Boxplot ", colnames(x.x)[i], sep = ""))
        dev.off()
    }
    
}