muma (version 1.4)

Plot.pca.loading: Plot PCA Loading Plot

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'

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)
  }