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hit_svd.R
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hit_svd.R
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perform_svd <- function(data, colorData, colorDataDim, colorLabel) {
dataMatrix <- read.table(data, row.names = 1)
(s <- svd(dataMatrix))
u <- s$u
v <- s$v
d <- s$d
write.table(u, file = paste(data, ".u", sep = ''))
write.table(v, file = paste(data, ".v", sep = ''))
write.table(d, file = paste(data, ".d", sep = ''))
png(filename = paste(data, ".d.png", sep = ''), res = 600, height = 3, width = 3, units = "in", pointsize = 6)
plot(1:length(s$d), s$d, xlab = "component number", ylab = "singular value", cex.axis = 1.5, cex.lab = 1.5)
dev.off()
setEPS()
postscript(paste(data, ".d.eps", sep = ''))
plot(1:length(s$d), s$d, xlab = "component number", ylab = "singular value", cex.axis = 1.5, cex.lab = 1.5)
dev.off()
png(filename = paste(data, ".v.png", sep = ''), res = 600, height = 3, width = 3, units = "in", pointsize = 6)
plot(s$v[,1], s$v[,2], xlab = "factor 1", ylab = " factor 2", cex.axis = 1.5, cex.lab = 1.5)
dev.off()
setEPS()
postscript(paste(data, ".v.eps", sep = ''))
plot(s$v[,1], s$v[,2], xlab = "factor 1", ylab = " factor 2", cex.axis = 1.5, cex.lab = 1.5)
dev.off()
png(filename = paste(data, ".v_id.png", sep = ''), res = 600, height = 3, width = 3, units = "in", pointsize = 6)
plot(s$v[,1], s$v[,2], xlab = "factor 1", ylab = " factor 2", cex.axis = 1.5, cex.lab = 1.5)
text(s$v[,1], s$v[,2], labels = seq_along(s$v[,1]), pos = 1)
dev.off()
setEPS()
postscript(paste(data, ".v_id.eps", sep = ''))
plot(s$v[,1], s$v[,2], xlab = "factor 1", ylab = " factor 2", cex.axis = 1.5, cex.lab = 1.5)
text(s$v[,1], s$v[,2], labels = seq_along(s$v[,1]), pos = 1)
dev.off()
colorMatrix <- read.csv(colorData, header = FALSE)
png(filename = paste(paste(paste(data, ".v_", sep = ''), colorLabel, sep = ''), ".png", sep = ''), res = 600, height = 3, width = 3, units = "in", pointsize = 6)
plot(s$v[,1], s$v[,2], xlab = "factor 1", ylab = " factor 2", col = rgb(log(1 + (colorMatrix[, colorDataDim] - colorMatrix[, colorDataDim][which.min(colorMatrix[, colorDataDim])])), 0, 0, maxColorValue = log(1 + (colorMatrix[, colorDataDim][which.max(colorMatrix[, colorDataDim])] - colorMatrix[, colorDataDim][which.min(colorMatrix[, colorDataDim])])), alpha = log(1 + (colorMatrix[, colorDataDim] - colorMatrix[, colorDataDim][which.min(colorMatrix[, colorDataDim])]))), pch = 19, cex = 1.5, cex.axis = 1.5, cex.lab = 1.5)
dev.off()
setEPS()
postscript(paste(paste(paste(data, ".v_", sep = ''), colorLabel, sep = ''), ".eps", sep = ''))
plot(s$v[,1], s$v[,2], xlab = "factor 1", ylab = " factor 2", col = rgb(log(1 + (colorMatrix[, colorDataDim] - colorMatrix[, colorDataDim][which.min(colorMatrix[, colorDataDim])])), 0, 0, maxColorValue = log(1 + (colorMatrix[, colorDataDim][which.max(colorMatrix[, colorDataDim])] - colorMatrix[, colorDataDim][which.min(colorMatrix[, colorDataDim])]))), pch = 19, cex = 1.5, cex.axis = 1.5, cex.lab = 1.5)
dev.off()
return (s)
}
arg <- commandArgs(trailingOnly = TRUE)
argLen <- length(arg)
if (argLen == 4) {
rawDataMatrix <- arg[1]
colorData <- arg[2]
colorDataDim <- as.numeric(arg[3])
colorLabel <- arg[4]
print(paste("Applying SVD on ", arg, " data...", sep = ''))
perform_svd(rawDataMatrix, colorData, colorDataDim, colorLabel)
}