predict.ptw: Prediction of warped signals

Description

Given a ptw object, predict either the signal at a certain warped time, or the warped time itself.

Usage

# S3 method for ptw
predict(object, newdata, what = c("response", "time"),
  RTref = NULL, …)

Arguments

object

An object of class "ptw"

newdata

Optional vector or matrix of new data points. If what equals "response", the new data should be a vector or matrix of intensities. If what equals "time", the new data is a vector of time points (a matrix of time points makes no sense...).

what

Either "response", in which case the function returns the warped signal, or "time", and then the function returns the warped time axis. That is, the time point in the warped sample corresponding to the given time point in the original sample.

RTref

Optional vector of retention times in the reference.

…

Further arguments, at the moment not used.

Value

The function returns a matrix (possibly containing only one row) of either warped time points or signals, warped according to the warping function defined in object. When warping signals individually, predict.ptw will check the dimension of newdata: if this is a vector or a matrix of one row, every single warping function will be applied to the one row. If the number of rows equals the number of warping functions, each row will be warped with its corresponding function. If the number of rows does not match the number of warping functions and is not equal to one, an error is given.

References

Eilers, P.H.C. "Parametric Time Warping." Anal. Chem., 2004, 76, 404-411

Bloemberg, T.G. et al. "Improved parametric time warping for proteomics." Chemom. Intell. Lab. Syst., 2010, 104, pp. 65-74

Examples

Run this code

# NOT RUN {
## educational example, contributed by zeehio (Sergio Oller)
x1 <- c(rep(0, 5), 1,1,1, 20, 40, 20, 1, 1, 1, rep(0, 5))
x2 <- c(rep(0, 6), 1,1,1, 20, 40, 20, 1, 1, 1, rep(0, 4))
time <- 1:length(x1)
## get time-warped object. Default: 'forward' warping, also works
## with backward warping
w1b <- ptw(ref = x1, samp = x2) 
## predict intensities of object x2 after warping at the times used in x1
x2wb <- predict(w1b, newdata = x2, what = "response")
## predict times where the original elements of x2 will end up
t2wb <- as.numeric(predict(w1b, newdata = time, what = "time"))

graphics.off()
par(mfrow = c(2,1))
plot(x1, type = "h", col = 2, lwd = 2, main = "Orig data")
points(x2, type = "h", col = 4)

plot(x1, type = "h", col = 2, lwd = 2, main = "Backward warping")
points(c(x2wb), type = "h", col = 4) # what = "response"
points(t2wb, x2, col = 4)            # what = "time"

## more relevant example
data(gaschrom)
## Global warping: all samples warped with the same function
ref <- gaschrom[1,]
samp <- gaschrom[14:16,]
gp <- ptw(ref, samp, init.coef = c(0, 1), warp.type = "global")
matplot(t(samp), type = "l", xlim = c(2200, 2400), lty = 1, col = 1:3)
lines(ref, type = "l", col = "gray", lwd = 2)
## plot predicted warped signal directly
matlines(t(predict(gp)), lty = 2, col = 1:3)
## plot original signal at warped time axis
matlines(t(predict(gp, newdata = 2001:2600, what = "time")),
         t(samp[,2001:2600]), col = 1:3, lwd = 3, lty = 2) ## OK
## result: good alignment with ref, differences between three profiles persist

## Individual warping: all samples warped individually
gp <- ptw(ref, samp, init.coef = c(0, 1), warp.type = "indiv")
predict(gp, what = "time", newdata = 2001:2600)
matplot(t(samp), type = "l", xlim = c(2200, 2400), lty = 1, col = 1:3)
lines(ref, type = "l", col = "gray", lwd = 2)
matlines(t(predict(gp, what = "time")),
         t(samp), col = 1:3, lty = 2)
## result: each individual profile is aligned to the ref

## How would samples 11:13 be warped using the coefficients from samples
## 14:16 (silly but just to make the point)?
samp.pred <- predict(gp, what = "response", newdata = gaschrom[11:13,])
# }