fitJumpDistHist: Fit jump distribution histogram

In jgodet/trackR: R tools and functions to compute jump analysis, describe and infer from single-molecule tracking data

Description

Fit jump distribution histogram

Usage

fitJumpDistHist(
  data,
  nbPop = 1,
  initHist = list(D2 = 200, D1 = 0.1),
  timeRes = 1,
  breaks = 100,
  xlim,
  ylim,
  xlab,
  main,
  ...
)

Arguments

data	dataframe with jump
nbPop	number of populations of diffusing species (1 or 2)
initHist	initialisation parameters for the nls fit for exmaple list(D2 = 200, D1=0.1) or list(D2 = .01, D1=.1, D3=10, D4=100)
timeRes	time resolution per unit of jump
breaks	binning of the histogram (number of breaks)

Author(s)

JuG

Examples

xmlPath <- "/Users/jgodet/Seafile/MaBibliotheque/Code/TrackMate/nmeth.2808-sv1.xml"
data <- readTrackMateXML(XMLpath = xmlPath)
data$jump<-jump(data, spaceRes=1)
fitJumpDistHist(data=data, nbPop = 1, initHist = list(D2 = 200,  D1=0.1))
fitJumpDistHist(data=data, xlim=c(0,10), col=rgb(.2,.2,.2,.2), main="test")
# Results are affected by the histogram binning
fitJumpDistHist(data=data, breaks = 30)
fitJumpDistHist(data=data, breaks = 150)
fitJumpDistHist(data=data, nbPop=3)
fitJumpDistHist(data=data, nbPop=2, initHist = list(D2 = .01,  D1=.1, D3=10, D4=100))

jgodet/trackR documentation built on May 24, 2020, 2:21 p.m.