plotTrack {sojourner} | R Documentation

## plotTrack

### Description

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

### Usage

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

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

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

    plotNucTrackOverlay(folder,trackll=NULL,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)

### Arguments

`resolution` | ratio of pixel to uM.
`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 createTrackll(folder, input, ab.track=TRUE).
`trackll` | a list of track lists.
`folder` | folder containing desired input data.
`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 track files (presumably it is the same folder with movie files).
`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.
`cores` | Number of cores to be used.
`trackll.sel` | Selected component trajectory output by selComponentTracks().
`input` | Input file type (Diatrack .txt file = 1; Diatrack .mat session file = 2; ImageJ .csv file = 3; SlimFast .txt file = 4).

### Details

- 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 Dcoef, 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.

### Value

- 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.

- csv Outputs csv file of the coordiantes of the trajectory, which users can use other plotting software (e.g. Prism or Excel) to plot tracks in their favor.

### Examples

    folder=system.file("extdata","SWR1",package="sojourner")
    trackll.ab=createTrackll(folder=folder, input=3, ab.track=TRUE)
    plotTrack(trackll.ab)

    ## plot from index file
    index.file=system.file("extdata","INDEX","indexFile.csv",
    package="sojourner")
    movie.folder=system.file("extdata","SWR1",package="sojourner")
    plotTrackFromIndex(index.file=index.file,movie.folder = movie.folder,
    input = 3)

    ## index file contain trajectories from multiple movie folders
    folder1=system.file("extdata","SWR1",package="sojourner")
    folder2=system.file("extdata","HTZ1",package="sojourner")
    index.file2=system.file("extdata","INDEX","indexFile2.csv",
    package="sojourner")
    plotTrackFromIndex(index.file=index.file2,
     movie.folder = c(folder1,folder2),
     input = 3)

    ## masking with image mask
    track.folder=system.file("extdata","SWR1_2",package="sojourner")
    trackll=createTrackll(folder=track.folder, input=3)
    trackll.masked <- maskTracks(folder=track.folder, trackll=trackll)
    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="sojourner")
    trackll=createTrackll(folder=folder2, input=3)

    ## use mergeTracks() for per folder comparison, the analsyis result
    ## can't be plot
    ##back to original image. To see component tracks on original nuclei image,
    ## do not use mergeTracks(), for per movie analysis.

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

    ## 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)
    set.seed(123)
    fit=fitNormDistr(
    dcoef,components=2,log.transform=TRUE,combine.plot=FALSE,output=FALSE)

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

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

[Package sojourner version 1.1.1 Index]