tests/iwpca.matrix.R

In HenrikBengtsson/aroma.light-BioC_release: Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types

library("aroma.light")

for (zzz in 0) {

# This example requires plot3d() in R.basic [http://www.braju.com/R/]
if (!require(pkgName <- "R.basic", character.only=TRUE)) break

# Simulate data from the model y <- a + bx + eps(bx)
x <- rexp(1000)
a <- c(2,15,3)
b <- c(2,3,4)
bx <- outer(b,x)
eps <- apply(bx, MARGIN=2, FUN=function(x) rnorm(length(x), mean=0, sd=0.1*x))
y <- a + bx + eps
y <- t(y)

# Add some outliers by permuting the dimensions for 1/10 of the observations
idx <- sample(1:nrow(y), size=1/10*nrow(y))
y[idx,] <- y[idx,c(2,3,1)]

# Plot the data with fitted lines at four different view points
opar <- par(mar=c(1,1,1,1)+0.1)
N <- 4
layout(matrix(1:N, nrow=2, byrow=TRUE))
theta <- seq(0,270,length=N)
phi <- rep(20, length.out=N)
xlim <- ylim <- zlim <- c(0,45);
persp <- list();
for (kk in seq(theta)) {
  # Plot the data
  persp[[kk]] <- plot3d(y, theta=theta[kk], phi=phi[kk], xlim=xlim, ylim=ylim, zlim=zlim)
}

# Weights on the observations
# Example a: Equal weights
w <- NULL
# Example b: More weight on the outliers (uncomment to test)
w <- rep(1, length(x)); w[idx] <- 0.8

# ...and show all iterations too with different colors.
maxIter <- c(seq(1,20,length=10),Inf)
col <- topo.colors(length(maxIter))
# Show the fitted value for every iteration
for (ii in seq(along=maxIter)) {
  # Fit a line using IWPCA through data
  fit <- iwpca(y, w=w, maxIter=maxIter[ii], swapDirections=TRUE)

  ymid <- fit$xMean
  d0 <- apply(y, MARGIN=2, FUN=min) - ymid
  d1 <- apply(y, MARGIN=2, FUN=max) - ymid
  b <- fit$vt[1,]
  y0 <- -b * max(abs(d0))
  y1 <-  b * max(abs(d1))
  yline <- matrix(c(y0,y1), nrow=length(b), ncol=2)
  yline <- yline + ymid

  for (kk in seq(theta)) {
    # Set pane to draw in
    par(mfg=c((kk-1) %/% 2, (kk-1) %% 2) + 1);
    # Set the viewpoint of the pane
    options(persp.matrix=persp[[kk]]);

    # Get the first principal component
    points3d(t(ymid), col=col[ii])
    lines3d(t(yline), col=col[ii])

    # Highlight the last one
    if (ii == length(maxIter))
      lines3d(t(yline), col="red", lwd=3)
  }
}

par(opar)

} # for (zzz in 0)
rm(zzz)