distanceToPlane {celltrackR}

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)

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.

Value

A single distance.

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" )