Plot.pca.loading: Plot PCA Loading Plot

In muma: Metabolomics Univariate and Multivariate Analysis

Description

This function is implemented in the unique function 'plot.pca'. It generated and visualizes PCA loading plot. This function cannot be used without having previously used the function 'explore.data'.

Usage

Plot.pca.loading(pcx, pcy, scaling)

Arguments

pcx	an integer indicating the principal component to be plotted in x.
pcy	an integer indicating the principal component to be plotted in y
scaling	a character string indicating the name of the scaling previously specified in the function 'explore.data'

Author(s)

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

Examples

	
## The function is currently defined as
function (pcx, pcy, scaling) 
{
    loadi = paste(getwd(), "/PCA_Data_", scaling, "/PCA_LoadingsMatrix.csv", 
        sep = "")
    Loading <- read.csv(loadi, sep = ",", header = TRUE)
    Loading.x <- Loading[, 2:ncol(Loading)]
    rownames(Loading.x) <- Loading[, 1]
    ppppp = paste(getwd(), "/PCA_Data_", scaling, "/PCA_P", sep = "")
    Pvar <- read.csv(ppppp, sep = ",", header = TRUE)
    Pvar.x <- Pvar[, 2:ncol(Pvar)]
    rownames(Pvar.x) <- Pvar[, 1]
    cum = Pvar[pcx, 2] + Pvar[pcy, 2]
    pca <- paste("Loadings PC", pcx, " (", Pvar[pcx, 2], ") %")
    pcb <- paste("Loadings PC", pcy, " (", Pvar[pcy, 2], ")%")
    lim.load = c()
    Max.pc1 = 1.1 * (max(Loading.x[, pcx]))
    Min.pc1 = 1.1 * (min(Loading.x[, pcx]))
    Mpc1 = c(Min.pc1 * 2, Max.pc1 * 2)
    Max.pc2 = 1.1 * (max(Loading.x[, pcy]))
    Min.pc2 = 1.1 * (min(Loading.x[, pcy]))
    Mpc2 = c(Min.pc2 * 2, Max.pc2 * 2)
    dev.new()
    plot(Loading.x[, pcx], Loading.x[, pcy], xlab = pca, ylab = pcb, 
        xlim = c(Min.pc1, Max.pc1), ylim = c(Min.pc2, Max.pc2), 
        main = paste("PCA Loading Plot (", scaling, ")", sep = ""), 
        sub = paste("Cumulative Proportion of Variance Explained = ", 
            cum, "%", sep = ""))
    axis(1, at = Mpc1, pos = c(0, 0), labels = FALSE, col = "grey", 
        lwd = 0.7)
    axis(2, at = Mpc2, pos = c(0, 0), labels = FALSE, col = "grey", 
        lwd = 0.7)
    text(Loading.x[, pcx], Loading.x[, pcy], labels = rownames(Loading.x), 
        cex = 0.6, pos = 1)
    E = paste(getwd(), "/PCA_Data_", scaling, "/LoadingPlot_PC", 
        pcx, "vsPC", pcy, ".pdf", sep = "")
    dev.copy2pdf(file = E)
  }

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