multiple-sample-visualization.R

source("load-cancer.R")
source("multiple-sample-visualization-functions.R")

imagesDirectory <- "images/multiple-sample-visualization/"

dir.create(imagesDirectory,
           recursive = TRUE,
           showWarnings = FALSE)

#	---------------------------------------------------------------------------
#
#	Intensity Matrix Visualization
#
#	---------------------------------------------------------------------------

library("gplots")

#
# The plotIntensityMatrix function is defined in the "multiple-sample-visualization-functions.R"
# source file
#
png(
  paste0(imagesDirectory, "intensity-matrix.png"),
  width = 1200,
  height = 800
)
plotIntensityMatrix(binnedPeaksMatrix)
dev.off()

#	---------------------------------------------------------------------------
#
#	Pairwise Spectra Comparison: visualization of shared and unshared peaks
#
#	---------------------------------------------------------------------------

a <- binnedPeaksMatrix[1, ]
b <- binnedPeaksMatrix[2, ]

col.onlyA <- "#7285a5"
col.onlyB <- "#4b560e"
col.both <- "#ff7369"

comparison.parts <- 6
comparison.lwd <- 2
masses <- as.numeric(colnames(binnedPeaksMatrix))
min.mass <- min(as.numeric(colnames(binnedPeaksMatrix)))
max.mass <- max(as.numeric(colnames(binnedPeaksMatrix)))
comparison.range <- (max.mass - min.mass) / comparison.parts

png(
  paste0(
    imagesDirectory,
    "spectra-comparison-multi-",
    comparison.parts,
    ".png"
  ),
  width = 1200,
  height = 800
)
par(
  mfrow = c(comparison.parts, 1),
  mar = c(2, 2, 2, 2),
  oma = c(4, 4, 4, 4)
)

for (part in 1:comparison.parts) {
  peak.start <- min.mass + (part - 1) * comparison.range
  peak.end <- min(max.mass, min.mass + part * comparison.range)
  
  indexes <-
    intersect(which(masses > peak.start), which(masses < peak.end))
  
  plot(
    NULL,
    xlim = c(peak.start, peak.end),
    ylim = c(0, 1),
    xlab = "m/z",
    ylab = NA,
    yaxt = "n"
  )
  
  for (index in 1:length(indexes)) {
    i <- indexes[index]
    if (a[i] > 0 && b[i] == 0) {
      abline(v = as.numeric(colnames(binnedPeaksMatrix)[i]),
             col = col.onlyA,
             lwd = comparison.lwd)
    } else if (a[i] == 0 && b[i] > 0) {
      abline(v = as.numeric(colnames(binnedPeaksMatrix)[i]),
             col = col.onlyB,
             lwd = comparison.lwd)
    } else if (a[i] > 0 && b[i] > 0) {
      abline(v = as.numeric(colnames(binnedPeaksMatrix)[i]),
             col = col.both,
             lwd = comparison.lwd)
    }
  }
}
dev.off()

#	---------------------------------------------------------------------------
#
#	Inverse Spectra Comparison
#
#	---------------------------------------------------------------------------

#
# The compareSpectra function is defined in the "multiple-sample-visualization-functions.R"
# source file
#

positive <- data$spectra[[1]]
negative <- data$spectra[[2]]

png(
  paste0(imagesDirectory, "inverse-comparison.png"),
  width = 1200,
  height = 800
)
compareSpectra(positive, negative)
dev.off()