celltrackR (version 1.2.1)

analyzeCellPairs: Find Distances and Angles for all Pairs of Tracks

Description

Find all pairs of cells and return the shortest distance between them at any point in time (if they share any time points), as well as the angle between their overall displacement vectors.

Usage

analyzeCellPairs(X, searchRadius = Inf, quietly = FALSE, ...)

Value

A dataframe with four columns: two for the indices of cellpairs, one for the distance between them, and one for their angle. Note that the distance will be NA for pairs of tracks that do not share time points, but their angle will still be computed.

Arguments

X

a tracks object

searchRadius

if specified, only return analysis for pairs of cells that are within distance searchRadius from each other at least at one point in time.

quietly

(default FALSE) if TRUE, suppress warnings

...

further arguments passed on to angleCells

Details

Analyzing track angles at different distances can be useful to detect directional bias or local crowding effects; see (Beltman et al, 2009).

Internally, the function uses cellPairs, angleCells, and distanceCells.

References

Joost B. Beltman, Athanasius F.M. Maree and Rob. J. de Boer (2009), Analysing immune cell migration. Nature Reviews Immunology 9, 789--798. doi:10.1038/nri2638

See Also

analyzeStepPairs to do something similar for single steps rather than entire tracks.

Examples

## Plot distance versus angle for all cell pairs. Sample T-cell data here for speed.
pairs <- analyzeCellPairs( sample( TCells, 100 ) )
scatter.smooth( pairs$dist, pairs$angle )