Motion Trajectory Analysis

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Documentation for package ‘celltrackR’ version 1.2.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

celltrackR-package	celltrackR: Quantitative analysis of motion.
aggregate	Compute Summary Statistics of Subtracks
aggregate.tracks	Compute Summary Statistics of Subtracks
analyzeCellPairs	Find Distances and Angles for all Pairs of Tracks
analyzeStepPairs	Find Distances and Angles for all Pairs of Steps
AngleAnalysis	Angle Analysis
angleCells	Angle between Two Tracks
angleSteps	Angle between Two Steps
angleToDir	Angle with a Reference Direction
angleToPlane	Angle with a Reference Plane
angleToPoint	Angle with a Reference Point
applyStaggered	Compute a Measure on a Track in a Staggered Fashion
as.data.frame.tracks	Convert Tracks to Data Frame
as.list.tracks	Convert from Tracks to List
as.tracks	Tracks Objects
as.tracks.data.frame	Convert from Data Frame to Tracks
as.tracks.list	Tracks Objects
asphericity	Track Measures
BCells	Two-Photon Data: B Cells in a Lymph Node
beaucheminTrack	Simulate a 3D Cell Track Using the Beauchemin Model
bootstrapTrack	Simulate Tracks via Bootstrapping of Speed and Turning Angle from a Real Track Dataset
boundingBox	Bounding Box of a Tracks Object
brownianTrack	Simulate an Uncorrelated Random Walk
c.tracks	Tracks Objects
cellPairs	Find Pairs of Tracks
celltrackR	celltrackR: Quantitative analysis of motion.
cheatsheet	Open the package cheat sheet
clusterTracks	Cluster Tracks
displacement	Track Measures
displacementRatio	Track Measures
displacementVector	Track Measures
distanceCells	Minimum Distance between Two Cells
distanceSteps	Distance between Two Steps
distanceToPlane	Distance to a Reference Plane
distanceToPoint	Distance to a Reference Point
duration	Track Measures
filterTracks	Filter Tracks
fractalDimension	Track Measures
get.immap.metadata	Get Track Metadata from ImmuneMap
get.immap.tracks	Read tracks from ImmuneMap
getFeatureMatrix	Obtaining A Feature Matrix
hotellingsTest	Test Unbiasedness of Motion
hurstExponent	Track Measures
interpolateTrack	Interpolate Track Positions
is.tracks	Tracks Objects
maxDisplacement	Track Measures
maxTrackLength	Length of Longest Track
meanTurningAngle	Track Measures
Neutrophils	Two-Photon Data: Neutrophils responding to an infection in the ear
normalizeToDuration	Normalize a Measure to Track Duration
normalizeTracks	Normalize Tracks
outreachRatio	Track Measures
overallAngle	Track Measures
overallDot	Track Measures
overallNormDot	Track Measures
pairsByTime	Distance between pairs of tracks at every timepoint
parse.immap.json	Read tracks from ImmuneMap
plot.tracks	Plot Tracks in 2D
plot3d	Plot Tracks in 3D
plotTrackMeasures	Bivariate Scatterplot of Track Measures
prefixes	Get Track Prefixes
projectDimensions	Extract Spatial Dimensions
read.immap.json	Read tracks from ImmuneMap
read.tracks.csv	Read Tracks from Text File
ReadImmuneMap	Read tracks from ImmuneMap
repairGaps	Process Tracks Containing Gaps
selectSteps	Get Single Steps Starting at a Specific Time from a Subset of Tracks
selectTracks	Select Tracks by Measure Values
simulateTracks	Generate Tracks by Simulation
sort.tracks	Sort Track Positions by Time
speed	Track Measures
splitTrack	Split Track into Multiple Tracks
squareDisplacement	Track Measures
staggered	Staggered Version of a Function
stepPairs	Find Pairs of Steps Occurring at the Same Time
straightness	Track Measures
subsample	Subsample Track by Constant Factor
subtracks	Decompose Track(s) into Subtracks
subtracksByTime	Extract Subtracks Starting at a Specific Time
TCells	Two-Photon Data: T Cells in a Lymph Node
timePoints	Find All Unique Time Points in a Track Dataset
timeStep	Compute Time Step of Tracks
trackFeatureMap	Dimensionality Reduction on Track Features
trackLength	Track Measures
TrackMeasures	Track Measures
tracks	Tracks Objects
vecAngle	Angle Between Two Vectors
wrapTrack	Create Track Object from Single Track