| 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)