iwpca: Fits an R-dimensional hyperplane using iterative re-weighted...

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

Description

Fits an R-dimensional hyperplane using iterative re-weighted PCA.

Usage

## S3 method for class 'matrix'
iwpca(X, w=NULL, R=1, method=c("symmetric", "bisquare", "tricube", "L1"), maxIter=30,
  acc=1e-04, reps=0.02, fit0=NULL, ...)

Arguments

X	N-times-K matrix where N is the number of observations and K is the number of dimensions.
w	An N vector of weights for each row (observation) in the data matrix. If NULL, all observations get the same weight.
R	Number of principal components to fit. By default a line is fitted.
method	If "symmetric" (or "bisquare"), Tukey's biweight is used. If "tricube", the tricube weight is used. If "L1", the model is fitted in L_1. If a function, it is used to calculate weights for next iteration based on the current iteration's residuals.
maxIter	Maximum number of iterations.
acc	The (Euclidean) distance between two subsequent parameters fit for which the algorithm is considered to have converged.
reps	Small value to be added to the residuals before the the weights are calculated based on their inverse. This is to avoid infinite weights.
fit0	A list containing elements vt and pc specifying an initial fit. If NULL, the initial guess will be equal to the (weighted) PCA fit.
...	Additional arguments accepted by wpca().

Details

This method uses weighted principal component analysis (WPCA) to fit a R-dimensional hyperplane through the data with initial internal weights all equal. At each iteration the internal weights are recalculated based on the "residuals". If method=="L1", the internal weights are 1 / sum(abs(r) + reps). This is the same as method=function(r) 1/sum(abs(r)+reps). The "residuals" are orthogonal Euclidean distance of the principal components R,R+1,...,K. In each iteration before doing WPCA, the internal weighted are multiplied by the weights given by argument w, if specified.

Value

Returns the fit (a list) from the last call to wpca() with the additional elements nbrOfIterations and converged.

Author(s)

Henrik Bengtsson

See Also

Internally wpca() is used for calculating the weighted PCA.

Examples

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)

HenrikBengtsson/aroma.light-BioC_release documentation built on May 7, 2019, 1:55 a.m.