plotTrack-methods: plotTrack
In sheng-liu/smt: Single Molecule Tracking

Description Usage Arguments Details Value Examples

Plot track/trajectory from track list. either randomly or specified.

plotTrack(ab.trackll,resolution=0.107,frame.min=8,frame.max=100,
          frame.start=1,frame.end=500)

plotTrackFromIndex(index.file, movie.folder=c(folder1,folder2,...),
                   resolution=0.107,frame.min=1,frame.max=100,
                   frame.start=1,frame.end=500)

plotTrackOverlay(trackll,max.pixel=128,nrow=2,ncol=2,width=16,height=16)

plotNucTrackOverlay(folder,trackll=NULL,mask=F,cores=1,
                    max.pixel=128,nrow=2,ncol=2,width=16,height=16)

plotComponentTrackOverlay(folder,trackll.sel=NULL,
                    max.pixel=128,nrow=2,ncol=2,width=16,height=16)

plotMask(folder,max.pixel=128,nrow=2,ncol=2,width=16,height=16)

`resolution`	ratio of pixel to µM.
`frame.min`	minimum frame number for plotting.
`frame.max`	max frame number for plotting.
`frame.start`	the first frame to plot. Default 1.
`frame.end`	last frame to plot. Default 500.
`ab.trackll`	absolute coordinates for plotting, generated from readDiatrack(folder,ab.track=T).
`index.file`	a csv file that contains index of tracks in the first column. Leave a header line when preparing such a file.
`movie.folder`	the path to the folder which contains Diatrack output txt files (presumably it is the same folder with movie files).
`mask.file`	path to the mask file.
`max.pixel`	Number of pixels of imaging regime.
`nrow`	Number of rows in the final plot.
`ncol`	Number of colums in the final plot.
`width`	Width of the page for plotting.
`height`	Height of the page for plotting.
`trackll.sel`	Selected component trajectory output by selComponentTracks().

plotTrackFromIndex: if user provide a csv file with first column listing the index of trajectories, this program will plot the tracks isted in the csv file. It is useful after manipulating with the output from Dceof, to plot the tracks that of interest to the user (e.g. highest Dcoef). User need to provide the indexFile.csv, and specify the movie folder which contains the movies where specified trajectories are tracked.
plotTrackOverlay: plot all tracks in trackll overlaid on one plot.
plotNucTrackOverlay: plot tracks in a movie overlayed with nuclei image. The nuclei image file must end with "_Nuclei.tif" to be recognized. If trackll is NULL (default), program will read in trackll from specified folder and return trackll, otherwise it will take the specified trackll directly.
plotComponentTrackOverlay: plot tracks base on component fitting of diffusion coefficient. Combined with selComponentTracks() function, together it allows select and plot tracks based on component fitting of track diffusion coefficient.
plotMask: plot image mask. The mask file name must ended with _MASK.tiff to be recognized.

PDF One PDF file with all the frames satisfy the creteria. If trackll has multiple items, it ouptus mutiple PDF files each corresponding to one item.

folder=system.file("extdata","SWR1",package="smt")
trackll.ab=readDiatrack(folder,ab.track=TRUE)
plotTrack(trackll.ab)

## plot from index file
index.file=system.file("extdata","INDEX","indexFile.csv",package="smt")
movie.folder=system.file("extdata","SWR1",package="smt")
plotTrackFromIndex(index.file=index.file,movie.folder = movie.folder)

## index file contain trajectories from multiple movie folders
folder1=system.file("extdata","SWR1",package="smt")
folder2=system.file("extdata","HTZ1",package="smt")
index.file2=system.file("extdata","INDEX","indexFile2.csv",package="smt")
plotTrackFromIndex(index.file=index.file2,movie.folder = c(folder1,folder2))

## masking with image mask
track.folder=system.file("extdata","SWR1_2",package="smt")
trackll=readDiatrack(folder=track.folder,merge=F,mask=F)
trackll.masked=readDiatrack(folder=track.folder,merge=F,mask=T)
str(trackll,1)
str(trackll.masked,1)

## compare the masking effect
plotTrackOverlay(trackll,nrow=1,ncol=1,width=8,height=8)
plotTrackOverlay(trackll.masked,nrow=1,ncol=1,width=8,height=8)

## compare masking effect with nuclei image
plotNucTrackOverlay(folder=track.folder,trackll,
                    nrow=1,ncol=1,width=8,height=8)
plotNucTrackOverlay(folder=track.folder,trackll.masked,
                    nrow=1,ncol=1,width=8,height=8)

## plot mask
plotMask(track.folder,nrow=1,ncol=1,width=8,height=8)


## plotComponentTrackOverlay (see selComponentTracks() for more details)
folder2=system.file("extdata","SWR1_2",package="smt")
trackll=readDiatrack(folder2,merge=F)

## use merge=T for per folder comparison, the analsyis result can't be plot
back to original image. To see component tracks on original nuclei image,
set merge=F, for per movie analysis.

## compute MSD
MSD=msd(trackll=trackll,plot=T)
msd(trackll=trackll,summarize=T,plot=T)

## calculate Dcoef
dcoef=Dcoef(MSD=MSD,method="static",plot=TRUE)

## fit normal distribution to define component
## set seed to reproduce results (see fitNormalDistr() for details on seed)
fit=fitNormDistr(
       dcoef,components=2,log.transform=T,combine.plot=F,output=F,seed=481)

## select component tracks based on fitting
trackll.sel=selComponentTracks(
      fit=fit,likelihood = 0.9,dcoef = dcoef,log.transformed = T,output = F)

## plot component tracks
plotComponentTrackOverlay(folder2,trackll.sel=trackll.sel)