selComponentTracks {sojourner} | R Documentation |
Select trajectory based on component fitting on diffusion coefficient.
selComponentTracks(trackll,fit,likelihood=0.9,dcoef, log.transformed=FALSE,output=FALSE)
trackll |
a list of track lists. |
fit |
Component fitting result form fitNormDistr() function. |
likelihood |
The likelihood of a trajecotry to be in fitted group. This parameter specifies the strigency of selecting trajectories to be in the fitted group and therefore influence the number of trajectories been selected. |
dcoef |
Diffusion coefficent calcualted by Dcoef, which provide the link between trajecotry index and diffusion coefficent. |
log.transformed |
A flag indicating if the fitting is been log transformed, select TRUE if fitting was done in fitNormDistr (log.transform = TRUE,..). This parameter will be removed in later version by directly read the info from the output of fitNormalDistr() function. |
output |
A logical indicating if output of selected trajectory index, which can be used for plot individual trajectory using plotTrack. |
combined list of trackll The result is a combined list of selected trajectories. The list is one level higher than trackll, use subsetting to output trackll.e.g. trackll[[1]], or trackll[['SWR1']].
## selComponentTracks() usage # 1. select componentTracks per folder (cross movie) using compareFolders # 2. select componentTracks per movie base, use plotComponentTracks to plot # component tracks back to initial Nuclei image. ## 1. select componentTracks per folder (cross movie) by using ## compareFolders folder1=system.file('extdata','SWR1',package='sojourner') folder2=system.file('extdata','HTZ1',package='sojourner') trackll=compareFolder(folders=c(folder1,folder2), input=3) MSD=msd(trackll=trackll) dcoef=Dcoef(MSD,dt=6,plot=FALSE,output=FALSE) # fit dcoef # for replication purpose set seed to fix number set.seed(484) fit=fitNormDistr(dcoef,components=2,log.transform=TRUE,combine.plot=FALSE, output=FALSE) # select component tracks from fitting trackll.sel=selComponentTracks(trackll=trackll,fit=fit,likelihood=0.9, dcoef=dcoef,log.transformed=TRUE,output=FALSE) # subset component tracks to further analyze msd, dcoef trackll.swr1=trackll.sel[['SWR1']] msd(trackll.swr1,plot=FALSE) msd(trackll.swr1,summarize=TRUE,plot=FALSE) Dcoef(trackll=trackll.swr1,plot=FALSE) plotTrackOverlay(trackll.swr1) # plotNucTrackOverlay(folder=folder1, trackll=trackll.swr1) dwellTime(trackll.swr1) # Output trajectory index to plot individually trackll.sel=selComponentTracks(trackll=trackll,fit=fit,likelihood = 0.9, dcoef = dcoef,log.transformed=TRUE, output=FALSE) # specify index file path. index.file=system.file('extdata','INDEX', 'componentTrackID-SWR1.comp.1.csv', package='sojourner') index.file2=system.file('extdata','INDEX', 'componentTrackID-SWR1.comp.2.csv', package='sojourner') movie.folder=system.file('extdata','SWR1_2',package='sojourner') plotTrackFromIndex(index.file=index.file,movie.folder = movie.folder, input = 3) plotTrackFromIndex(index.file=index.file2,movie.folder = movie.folder, input = 3) ## 2. select componentTracks per movie base, use plotComponentTracks to ##plot component tracks back to initial Nuclei image. ## plotComponentTrackOverlay folder3=system.file('extdata','SWR1_2',package='sojourner') trackll=createTrackll(folder=folder3, input=3) ## use merge=TRUE 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=FALSE (for ## per movie analysis) ## may not make much sense to msd on individual movie, ##however for plot component track back to original nuclei image. ## compute MSD MSD=msd(trackll=trackll,plot=FALSE) msd(trackll=trackll,summarize=TRUE,plot=FALSE) ## calculate Dcoef dcoef=Dcoef(MSD=MSD,method='static',plot=FALSE) ## fit normal distribution to define component ## set seed to reproduce results (see fitNormalDistr() for details on seed) set.seed(484) fit=fitNormDistr(dcoef,components=2,log.transform=TRUE,combine.plot=FALSE, output=FALSE) ## select component tracks based on fitting trackll.sel=selComponentTracks(trackll=trackll,fit=fit,likelihood = 0.9, dcoef) ## plot component tracks plotComponentTrackOverlay(folder=folder3,trackll.sel=trackll.sel)