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celltrackR (version 1.1.0)

Motion Trajectory Analysis

Description

Provides methodology to analyze cells that move in a two- or three-dimensional space. Available measures include displacement, confinement ratio, autocorrelation, straightness, turning angle, and fractal dimension. Measures can be applied to entire tracks, steps, or subtracks with varying length. While the methodology has been developed for cell trajectory analysis, it is applicable to anything that moves including animals, people, or vehicles. Some of the methodology implemented in this packages was described by: Beauchemin, Dixit, and Perelson (2007) , Beltman, Maree, and de Boer (2009) , Gneiting and Schlather (2004) , Mokhtari, Mech, Zitzmann, Hasenberg, Gunzer, and Figge (2013) , Moreau, Lemaitre, Terriac, Azar, Piel, Lennon-Dumenil, and Bousso (2012) , Textor, Peixoto, Henrickson, Sinn, von Andrian, and Westermann (2011) , Textor, Sinn, and de Boer (2013) , Textor, Henrickson, Mandl, von Andrian, Westermann, de Boer, and Beltman (2014) .

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Version

Install

install.packages('celltrackR')

Monthly Downloads

304

Version

1.1.0

License

GPL-2

Maintainer

Johannes Textor

Last Published

March 21st, 2022

Functions in celltrackR (1.1.0)

Two-Photon Data: Neutrophils in an Infected Lung

aggregate.tracks

Compute Summary Statistics of Subtracks

analyzeCellPairs

Find Distances and Angles for all Pairs of Tracks

Angle with a Reference Point

analyzeStepPairs

Find Distances and Angles for all Pairs of Steps

Angle with a Reference Plane

Angle with a Reference Direction

Compute a Measure on a Track in a Staggered Fashion

Simulate an Uncorrelated Random Walk

Find Pairs of Tracks

Two-Photon Data: B Cells in a Lymph Node

normalizeToDuration

Normalize a Measure to Track Duration

normalizeTracks

Normalize Tracks

Simulate Tracks via Bootstrapping of Speed and Turning Angle from a Real Track Dataset

Bounding Box of a Tracks Object

celltrackR: Quantitative analysis of motion.

Open the package cheat sheet

Generate Tracks by Simulation

Sort Track Positions by Time

as.data.frame.tracks

Convert Tracks to Data Frame

Plot Tracks in 2D

Distance between pairs of tracks at every timepoint

Angle between Two Steps

Angle between Two Tracks

Convert from Tracks to List

Angle Between Two Vectors

Plot Tracks in 3D

Create Track Object from Single Track

Get Single Steps Starting at a Specific Time from a Subset of Tracks

plotTrackMeasures

Bivariate Scatterplot of Track Measures

Select Tracks by Measure Values

Find All Unique Time Points in a Track Dataset

Compute Time Step of Tracks

as.tracks.data.frame

Convert from Data Frame to Tracks

beaucheminTrack

Simulate a 3D Cell Track Using the Beauchemin Model

distanceToPoint

Distance to a Reference Point

Minimum Distance between Two Cells

Get Track Prefixes

projectDimensions

Extract Spatial Dimensions

Split Track into Multiple Tracks

Length of Longest Track

interpolateTrack

Interpolate Track Positions

Decompose Track(s) into Subtracks

Staggered Version of a Function

getFeatureMatrix

Obtaining A Feature Matrix

Test Unbiasedness of Motion

read.tracks.csv

Read Tracks from Text File

Distance between Two Steps

distanceToPlane

Distance to a Reference Plane

subtracksByTime

Extract Subtracks Starting at a Specific Time

Process Tracks Containing Gaps

Find Pairs of Steps Occurring at the Same Time

Subsample Track by Constant Factor

trackFeatureMap

Dimensionality Reduction on Track Features

Two-Photon Data: T Cells in a Lymph Node