# efg, 6 Oct 2005
# based on examples in prada documentation

library(prada)
filepath <- system.file("extdata", "fas Bcl2 plate323-04-04.A01", package = "prada")
filepath
sampdat <- readFCS(filepath)
fdat <- exprs(sampdat)
dim(fdat)
colnames(fdat)

# 1. Plot raw data
plot(fdat[, "FSC-H"], fdat[, "SSC-H"],
     pch = 20, col = "#303030",
     xlab = "FSC",
     ylab = "SSC",
     main = "Scatter plot FSC vs SSC")


# 2. Show selections for various scale factors
savepar <- par(mfrow=c(2,2))
for (ScaleFactor in c(1.0, 1.5, 2.0, 2.5))
{
  nfit <- fitNorm2(fdat[, "FSC-H"], fdat[, "SSC-H"], scalefac = ScaleFactor)
  plotNorm2(nfit, selection = TRUE, ellipse = TRUE,
    xlab="FSC-H", ylab="SSC-H",
    main=paste("SSC-H vs. FSC-H (ScaleFactor=",ScaleFactor,")", sep=""))
}
par(savepar)


# 3. Let's select and plot ONLY the points for ScaleFactor=2
nfit <- fitNorm2(fdat[, "FSC-H"], fdat[, "SSC-H"], scalefac=2.5)
cleanfdat <- fdat[nfit$sel, ]

xlim <- range(fdat[, "FSC-H"])
ylim <- range(fdat[, "SSC-H"])
plot(fdat[, "FSC-H"], fdat[, "SSC-H"], pch = 20, col = "#303030",
  xlab = "FSC-H", ylab = "SSC-H", main = "all data", xlim = xlim,
  ylim = ylim)

plot(cleanfdat[, "FSC-H"], cleanfdat[, "SSC-H"],
     pch = 20, col = "#303030",
     xlab = "FSC-H",
     ylab = "SSC-H",
     main = "clean data only",
     xlim = xlim, ylim = ylim)


# 4. Try smoothScatter
require(geneplotter)
smoothScatter(fdat[, c("FSC-H", "SSC-H")], nrpoints = 100)
smoothScatter(fdat[, c("FSC-H", "SSC-H")], nrpoints = Inf)