celltrackR (version 1.2.1)

distanceToPlane: Distance to a Reference Plane

Description

Compute the (shortest) distance between the starting point of a track and a reference plane. Useful to detect directed movement and/or tracking artefacts.

Usage

distanceToPlane(x, p1 = c(0, 0, 0), p2 = c(0, 1, 0), p3 = c(1, 0, 0), from = 1)

Value

A single distance.

Arguments

x

a single input track; a matrix whose first column is time and whose remaining columns are a spatial coordinate.

p1, p2, p3

numeric vectors of coordinates of three points specifying a reference plane to compute distances to.

from

index, or vector of indices, of the first row of the track. If from is a vector, distances are returned for all steps starting at the indices in from.

See Also

angleToPlane to compute the angle to the plane, and AngleAnalysis for other methods to compute angles and distances.

Examples

## Plotting the angle versus the distance to a reference plane can be informative to
## detect tracking artefacts near the border of the imaging volume.
## We should be suspicious especially when small angles are more frequent at low distances
## to the border planes.
load( system.file("extdata", "TCellsRaw.rda", package="celltrackR" ) )
steps <- subtracks( TCellsRaw, 1 )
minz <- boundingBox( TCellsRaw )["min","z"]
## Compute angles and distances to the lower plane in z-dimension
angles <- sapply( steps, angleToPlane, p1 = c(0,0,minz), p2 = c(1,0,minz), p3 = c(0,1,minz) )
distances <- sapply( steps, distanceToPlane, p1 = c(0,0,minz), p2 = c(1,0,minz), p3 = c(0,1,minz) )
scatter.smooth( distances, angles )
abline( h = 32.7, col = "red" )