R/stocsy.1d.R

In muma: Metabolomics Univariate and Multivariate Analysis

stocsy.1d <-
function(scaling, driver.peak) {
  pwd.n = paste(getwd(), "/Preprocessing_Data_", scaling, "/ProcessedTable.csv", sep="")
  x <- read.csv(pwd.n, sep=",", header=TRUE)
  x.x <- x[,2:ncol(x)]
  rownames(x.x) <- x[,1]
  x.t <- x.x
  mycor = cor(x.t, method=c("pearson"))
  library(gplots)
  pal = matrix(rich.colors(41), nrow=1)
  sec = matrix(seq(-1,1,0.05), nrow=1)
  d = matrix(mycor[,driver.peak], ncol=1)
  sec40 = ncol(sec)-1
  col=c()
  for (i in 1:nrow(d)) {
	for (j in 1:sec40) {
		if (sec[,j] <= d[i,] & d[i,] <= sec[,j+1]) {
			col = matrix(c(col, pal[,j]), ncol=1)
		}
	}
  }
  plot(mycor[,driver.peak], type="h", col=col, xlab = "Variables", ylab = paste("Coefficient of correlation with ", rownames(x.x)[driver.peak], sep=""), main = paste("STOCSY 1D (", rownames(x.x)[driver.peak], ")", sep=""), ylim = c(-1,1))
  text(mycor[,driver.peak], labels=colnames(x.x), cex=0.5, col=col)  
  dirout = paste(getwd(), "/STOCSY_1D/", sep="")
  dir.create(dirout)
  out = paste(dirout, "stocsy_1d_", colnames(x.x)[driver.peak], ".pdf", sep="")
  dev.copy2pdf(file=out)
  }