celltrackR (version 1.2.1)

applyStaggered: Compute a Measure on a Track in a Staggered Fashion

Description

Computes a measure on all subtracks of a track and return them either as a matrix or return their mean.

Usage

applyStaggered(x, measure, matrix = FALSE, min.segments = 1)

Value

If matrix is set, a matrix with the values of the measure for all the input track's subtracks is returned. The value of this matrix at position [i, j] corresponds to the subtrack that starts with the input track's \(j\)th point and ends at its \(i\)th. Thus, with increasing column number, the regarded subtrack's starting point is advanced on the original track, and the values for increasingly long subtracks starting from this point can be found columnwise below the main diagonal, respectively. If `matrix` is not set, the mean over the values of the measure for all subtracks of at least `min.segments` segments is retruned.

Arguments

x

the track for which the measure is to be computed.

measure

the measure that is to be computed.

matrix

a logical indicating whether the whole matrix of values for the measure for each of the input track's subtracks is to be returned. Otherwise only the mean is returned.

min.segments

the number of segments that each regarded subtrack should at least consist of. Typically, this value would be set to the minimum number of segments that a (sub)track must have in order for the measure to be decently computed. For example, at least two segments are needed to compute the overallAngle.

Details

The measure is computed for each of the input track's subtracks of length at least min.segments, and the resulting values are either returned in a matrix (if matrix is set), or their mean is returned. The computed matrix is symmetric since the direction along which a track is traversed is assumed not to matter. The values at [i, i + j], where j is a nonnegative integer with \(j < \)min.segments, (with the default value min.segments=1 this is exactly the main diagonal) are set to NA.

Examples

## Compute the staggered matrix for overallAngle applied to all long enough
## subtracks of the first T cell track
applyStaggered(TCells[[1]], overallAngle, matrix=TRUE, min.segments = 2)