wpca: Light-weight Weighted Principal Component Analysis

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

Description

Calculates the (weighted) principal components of a matrix, that is, finds a new coordinate system (not unique) for representing the given multivariate data such that i) all dimensions are orthogonal to each other, and ii) all dimensions have maximal variances.

Usage

## S3 method for class 'matrix'
wpca(x, w=NULL, center=TRUE, scale=FALSE, method=c("dgesdd", "dgesvd"),
  swapDirections=FALSE, ...)

Arguments

x	An NxK matrix.
w	An N vector of weights for each row (observation) in the data matrix. If NULL, all observations get the same weight, that is, standard PCA is used.
center	If TRUE, the (weighted) sample mean column vector is subtracted from each column in mat, first. If data is not centered, the effect will be that a linear subspace that goes through the origin is fitted.
scale	If TRUE, each column in mat is divided by its (weighted) root-mean-square of the centered column, first.
method	If "dgesdd" LAPACK's divide-and-conquer based SVD routine is used (faster [1]). If "dgesvd", LAPACK's QR-decomposition-based routine is used.
swapDirections	If TRUE, the signs of eigenvectors that have more negative than positive components are inverted. The signs of corresponding principal components are also inverted. This is only of interest when for instance visualizing or comparing with other PCA estimates from other methods, because the PCA (SVD) decompostion of a matrix is not unique.
...	Not used.

Value

Returns a list with elements:

pc	An NxK matrix where the column vectors are the principal components (a.k.a. loading vectors, spectral loadings or factors etc).
d	An K vector containing the eigenvalues of the principal components.
vt	An KxK matrix containing the eigenvector of the principal components.
xMean	The center coordinate.

It holds that x == t(t(fit$pc %*% fit$vt) + fit$xMean).

Method

A singular value decomposition (SVD) is carried out. Let X=mat, then the SVD of the matrix is X = U D V', where U and V are othogonal, and D is a diagonal matrix with singular values. The principal returned by this method are U D.

Internally La.svd() (or svd()) of the base package is used. For a popular and well written introduction to SVD see for instance [2].

Author(s)

Henrik Bengtsson

References

[1] J. Demmel and J. Dongarra, DOE2000 Progress Report, 2004. http://www.cs.berkeley.edu/~demmel/DOE2000/Report0100.html
[2] Todd Will, Introduction to the Singular Value Decomposition, UW-La Crosse, 2004. http://www.uwlax.edu/faculty/will/svd/

See Also

For a iterative re-weighted PCA method, see iwpca(). For Singular Value Decomposition, see svd(). For other implementations of Principal Component Analysis functions see (if they are installed): prcomp in package stats and pca() in package pcurve.

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

# -------------------------------------------------------------
# A first example
# -------------------------------------------------------------
# Simulate data from the model y <- a + bx + eps(bx)
x <- rexp(1000)
a <- c(2,15,3)
b <- c(2,3,15)
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 1/3 of the observations
idx <- sample(1:nrow(y), size=1/3*nrow(y))
y[idx,] <- y[idx,c(2,3,1)]

# Down-weight the outliers W times to demonstrate how weights are used
W <- 10

# Plot the data with fitted lines at four different view points
N <- 4
theta <- seq(0,180,length=N)
phi <- rep(30, length.out=N)

# Use a different color for each set of weights
col <- topo.colors(W)

opar <- par(mar=c(1,1,1,1)+0.1)
layout(matrix(1:N, nrow=2, byrow=TRUE))
for (kk in seq(theta)) {
  # Plot the data
  plot3d(y, theta=theta[kk], phi=phi[kk])
 
  # First, same weights for all observations
  w <- rep(1, length=nrow(y))

  for (ww in 1:W) {
    # Fit a line using IWPCA through data
    fit <- wpca(y, w=w, swapDirections=TRUE)
 
    # Get the first principal component
    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
 
    points3d(t(ymid), col=col)
    lines3d(t(yline), col=col)

    # Down-weight outliers only, because here we know which they are.
    w[idx] <- w[idx]/2
  }

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

par(opar)

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


  if (dev.cur() > 1) dev.off()

  # -------------------------------------------------------------
# A second example
# -------------------------------------------------------------
# Data
x <- c(1,2,3,4,5)
y <- c(2,4,3,3,6)

opar <- par(bty="L")
opalette <- palette(c("blue", "red", "black"))
xlim <- ylim <- c(0,6)

# Plot the data and the center mass
plot(x,y, pch=16, cex=1.5, xlim=xlim, ylim=ylim)
points(mean(x), mean(y), cex=2, lwd=2, col="blue")


# Linear regression y ~ x
fit <- lm(y ~ x)
abline(fit, lty=1, col=1)

# Linear regression y ~ x through without intercept
fit <- lm(y ~ x - 1)
abline(fit, lty=2, col=1)


# Linear regression x ~ y
fit <- lm(x ~ y)
c <- coefficients(fit)
b <- 1/c[2]
a <- -b*c[1]
abline(a=a, b=b, lty=1, col=2)

# Linear regression x ~ y through without intercept
fit <- lm(x ~ y - 1)
b <- 1/coefficients(fit)
abline(a=0, b=b, lty=2, col=2)


# Orthogonal linear "regression"
fit <- wpca(cbind(x,y))

b <- fit$vt[1,2]/fit$vt[1,1]
a <- fit$xMean[2]-b*fit$xMean[1]
abline(a=a, b=b, lwd=2, col=3)

# Orthogonal linear "regression" without intercept
fit <- wpca(cbind(x,y), center=FALSE)
b <- fit$vt[1,2]/fit$vt[1,1]
a <- fit$xMean[2]-b*fit$xMean[1]
abline(a=a, b=b, lty=2, lwd=2, col=3)

legend(xlim[1],ylim[2], legend=c("lm(y~x)", "lm(y~x-1)", "lm(x~y)",
          "lm(x~y-1)", "pca", "pca w/o intercept"), lty=rep(1:2,3),
                     lwd=rep(c(1,1,2),each=2), col=rep(1:3,each=2))

palette(opalette)
par(opar)

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