angleToPlane | R Documentation |
Compute the angle between a track's overall displacement and a reference plane. Useful to detect directed movement and/or tracking artefacts.
angleToPlane( x, p1 = c(0, 0, 0), p2 = c(0, 1, 0), p3 = c(1, 0, 0), from = 1, degrees = TRUE )
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
|
degrees |
logical; should angles be returned in degrees rather than radians? (default = TRUE). |
The average angle of steps to a reference plane should be roughly 32.7 degrees. Lower angles to the border planes of an imaging volume can be indicative of tracking artefacts, and systematic deviations from 32.7 can indicate a directional bias (Beltman et al, 2009).
A single angle.
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
distanceToPlane
to compute the distance to the reference plane, and
AngleAnalysis
for other methods to compute angles and distances.
## 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" )
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