displacementCDF-methods: displacementCDF
In snjy9182/smt-beta: Statistical analysis of single molecule trajectories

Description Usage Arguments Details Value Examples

calculate cumulative distribution function of all displacement for individual trajectories.

1 2	displacementCDF(trackll,dt=1,resolution=0.107,plot=FALSE,output=FALSE, bivar=FALSE)

`dt`	Time intervals.
`resolution`	ratio of pixel to uM.
`bivar`	bivar=FALSE, view displacement r as single variable; bivar=TRUE, view x,y as bivarate. Default value F.
`trackll`	a list of track lists.
`plot`	An logical indicate if plot should be generated. See Values for detail.
`output`	An logical indicate if output should be generated. See Values for detail.

The cumulative radial distribution function, P(r, i*dt), is the probability of finding the diffusing particle within a radius r from the origin at time lag i*dt:

P(r,i*dt) = 1 - e^(-r^2/4*D*(i*dt))

the CDF and UniqueDisplacement in the output file is corresponding to P and r in this formula. If intend to generate the CDF plot from the output file, the CDF and UniqueDisplacement is corresponding to the y and x values in the CDF output plot.

list of "stepwise.displacement" and "CDF.displacement", A list of stepwise.displacement" and "CDF.displacement". the name of the list is the track folder name.
Output file, Displacement of individual trajectoreis at specified dt. The output file is for user to plot in other applications. The column "UniqueDisplacement" is the x axis, and column "CDF" is the y axis for a CDF plot. The distribution of "UniqueDisplacement" is the density plot.
CDF plot, CDF plot of displacement for individual files.

folder1=system.file("extdata","SWR1",package="sojourner")
folder2=system.file("extdata","HTZ1",package="sojourner")
trackll=compareFolder(folders=c(folder1,folder2), input=3)
displacementCDF(trackll,dt=1,plot=TRUE)