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#' A function to get the dynamic time warping between SHAPE trace magnitudes.
#' @title getTimeWarping
#' @aliases getTimeWarping
#' @keywords getTimeWarping change RNA
#' @usage getTimeWarping(sample, base=sample[1,], margin=1)
#' @param sample A numeric matrix containing values to be compared (e.g. a set of mutant SHAPE traces).
#' @param base An optional numeric vector containing the values to which the samples are to be compared (e.g. a wildtype SHAPE trace). Default is the first trace in sample.
#' @param margin An optional number indicating if the samples are organized by rows or columns, where 1 indicates rows and 2 indicates columns. Default is 1.
#' @export
#' @import dtw
#' @details This function calculates the dynamic time warping between the base vector and each row (or column) in sample.
#' @return A numeric vector of time warping values.
#' @author Chanin Tolson
#' @seealso \code{\link{getFeatures}}
#' @examples #sample data
#' sample = matrix(sample(1:100), ncol=10)
#' #normalize
#' samp_norm = normalize(sample)
#' #reduce noise
#' samp_nreduce = reduceNoise(samp_norm, trim=1, high=4)
#' #get time warping
#' tw = getTimeWarping(samp_nreduce)
#'
getTimeWarping = function(sample, base=sample[1,], margin=1){
#set optional paramater margin
if(missing(margin)) {
margin = 1
} else {
if(!(margin %in% c(1,2))){
warning("Margin value not valid. Margin set to default.")
margin = 1
}
if(margin==2){
sample = t(sample)
}
}
#set optional paramater base
if(missing(base)) {
base = sample[1,]
} else {
base = base
}
#remove NA values
s = sample
b = base
base[which(is.na(sample),arr.ind=T)[1]]=0
sample[,is.na(base)]=0
sample[is.na(sample)]=0
base[is.na(base)]=0
#calculate timewarp change
timewarp = function(x, y){
warp = dtw(x, y, distance.only=T)
return(warp$normalizedDistance)
}
if(dim(sample)[1]==1){
tw = dtw(as.vector(sample[1,]), as.vector(base))$normalizedDistance
} else{
tw = apply(sample, 1, timewarp, y=base)
}
#return time warping
return(tw)
}
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