box.plot: Generate box plots

In muma: Metabolomics Univariate and Multivariate Analysis

Description

Generates box plots of each variable (column) present in the matrix provided and according to the class specification provided

Usage

box.plot(file)

Arguments

file	a connection or a character string giving the name of the file containing information to plot

Details

This function can be used by calling the function 'univariate', in which 'box.plot' is implemented. The groups are distinguished according to the class vector provided within the dataset. In particular, the file provided has to be formatted with the first column indicating the name of each sample and the second column indicating the class of belonging of each sample.

Value

A list of box plots is generated and written in a directory called 'BoxPlot', within the directory 'Univariate' (generated by the function 'univariate'), in the working directory.

Author(s)

Edoardo Gaude, Dimitrios Spiliotopoulos, Francesca Chignola, Silvia Mari, Andrea Spitaleri and Michela Ghitti

See Also

univariate

Examples

## The function is currently defined as
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)
    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] ~ x.x[, 1], boxfill = c(seq(1, NoF)), 
            ylab = colnames(x.x)[i], xlab = "Groups", border = "grey30", 
            main = paste("Boxplot ", colnames(x.x)[i], sep = ""))
        dev.off()
    }
  }

muma documentation built on May 2, 2019, 9:45 a.m.