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%- Also NEED an '\alias' for EACH other topic documented here.
\title{Plotting of dynamic time warp results: annotated warping function}
  Display the query and reference time series and their warping curve,
  arranged for visual inspection. 


	        margin=4, inner.margin=0.2, title.margin=1.5,
	        xlab="Query index",ylab="Reference index",main="Timeseries alignment",
			... )

%- maybe also 'usage' for other objects documented here.
  \item{d}{ an alignment result, object of class \code{dtw}}
  \item{xts}{ query vector }
  \item{yts}{  reference vector }
  \item{xlab}{ label for the query axis}
  \item{ylab}{label for the reference axis}
  \item{main}{main title}
  \item{type.align}{line style for warping curve plot}
  \item{type.ts}{line style for timeseries plot}
  \item{match.indices}{indices for which to draw a visual
  \item{margin}{outer figure margin }
  \item{inner.margin}{inner figure margin }
  \item{title.margin}{space on the top of figure}
  \item{...}{additional arguments, used for the warping curve}


  The query time series is plotted in the bottom panel, with indices
  growing rightwards and values upwards. Reference is in the left panel,
  indices growing upwards and values leftwards. The warping curve panel
  matches indices, and therefore element (1,1) will be at the lower
  left, (N,M) at the upper right.

  Argument \code{match.indices} is used to draw a visual guide to
  matches; if a vector is given, guides are drawn for the corresponding
  indices in the warping curve (match lines). If integer, it is used as
  the number of guides to be plotted. The corresponding style is
  customized via the \code{match.col} and \code{match.lty} arguments.

  If \code{xts} and \code{yts} are not supplied, they will be recovered
  from \code{d}, as long as it was created with the two-argument call of
  \code{\link{dtw}} with \code{keep.internals=T}.  Only single-variate
  time series can be plotted.


\author{Toni Giorgino }

\section{Warning}{ The function is incompatible with mechanisms for
     arranging plots on a device: \code{par(mfrow)}, \code{layout} and
     \code{split.screen}. Appearance of the match lines and timeseries
     currently  can not be customized. }


## A noisy sine wave as query
## A cosine is for reference; sin and cos are offset by 25 samples


## Beware of the reference's y axis, may be confusing
## Equivalent to plot(alignment,type="three");

## Highlight matches of chosen QUERY indices. We will do some index
## arithmetics to recover the corresponding indices along the warping
## curve

hq <- (0:8)/8              
hq <- round(hq*100)      #  indices in query for  pi/4 .. 7/4 pi

hw <- (alignment$index1 \%in\% hq)   # where are they on the w. curve?
hi <- (1:length(alignment$index1))[hw];   # get the indices of TRUE elems



\concept{Dynamic Time Warp}

\keyword{ hplot }

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