Calculation of the JD of multiple tracks. Calculation is equivalent to a single time lag point on the ensemble MSD curve, typically represented as a histogram Input is a data frame of tracks imported using readTrackMateXML() The default time step is one frame - which is the equivalent to the plot generated to show displacement versus time.
Usage
calculateJD(
dataList,
deltaT = 1,
nPop = 2,
mode = "ECDF",
init = NULL,
timeRes = 1,
breaks = 100
)Arguments
- dataList
list of data frame (must include at a minimum - trace (track ID), x, y and t (in real coords)) and calibration
- deltaT
integer to represent the multiple of frames that are to be analysed
- nPop
integer (either 1,2 or 3) number of populations for the jump distance fitting
- mode
string indicated ECDF (default) or hist (histogram)
- init
initialisation parameters for the nls fit for example list(D2 = 200, D1 = 0.1) or list(D2 = 0.01, D1=0.1, D3=10, D4=100)
- timeRes
time resolution per unit of jump. Frame interval is 0.5 s and jump interval is two steps, timeRes = 1.
- breaks
number of bins for histogram. With ECDF breaks can be high e.g. 100, for mode = "hist" they should be low, perhaps 30.
Value
a list of data frame of jump distances, NAs removed; and a list of parameters called jumpParam (jumptime, deltaT, nPop)
Examples
xmlPath <- system.file("extdata", "ExampleTrackMateData.xml", package="TrackMateR")
tmObj <- readTrackMateXML(XMLpath = xmlPath)
#> Units are: 1 pixel and 0.07002736 s
#> Spatial units are in pixels - consider transforming to real units
#> Extracting spot data...
#> Matching track data...
#> Calculating distances...
tmObj <- correctTrackMateData(tmObj, xyscalar = 0.04)
#> Correcting XY scale.
jdObj <- calculateJD(dataList = tmObj, deltaT = 2)