Caclulate diffusion coefficient (Dcoef) for trajecotries.
Dcoef( MSD=NULL,trackll=NULL,dt=6,filter=c(min=7,max=Inf),rsquare=0.8, resolution=0.107, binwidth=NULL, method=c('static','percentage','rolling.window'), plot=FALSE,output=FALSE,t.interval=0.01,profile=NULL)
Arguments
| MSD | Mean Square Displacement calculated using msd() function. Either MSD or trackll can be passed into Dcoef for calculation of diffusion coefficient. |
|---|---|
| trackll | Track list output from readDiatrack(). |
| dt | Time intervals. Default 6. |
| filter | a vector specifies the minimum and max length of trajecotries to be analyzed. Take only trajectories that has number of frames greater than (>=) min and less than (<) max. |
| rsquare | rsquare filter on Dcoef results. Default to be 0.8. Set value to 0 if rsquare filter is not desired. |
| resolution | ratio of pixel to uM. |
| binwidth | binwidth used for histogram. Default NULL, automatically assign binwidth. |
| method | 'static', uses time lags 2~5 to calculate diffusion coefficient; 'percentage', uses (tierd) percentage (default 0.25) of time lags (see Details). 'rolling.window', time lags uses for Dcoef follows a rolling window with specified window size (default 4). |
| plot | A parameter for plotting. Default FALSE, no plot; If TRUE, automatically plots 'histogram' with count information, binwidth can be set through parameter binwidth; as well as 'density' with density/frequency. |
| output | An Logical indicate if output should be generated. See Values for detail. |
| t.interval | time interval between frames, default 0.010 s (10ms). |
| profile | Location of preference file. By default (NULL), it is stored at : system.file('extdata','PREF','profile.csv',package='sojourner'). User can provide preference file by specifying the location of the file, e.g. profile='/Users/shengliu/Desktop/profile.csv'. |
Value
Dcoef A list of Dcoef for each file in trackll.
PDF Log.Dcoef histogram fitted with density curve, when plot = TRUE.
csv Dcoef output in csv format, when output = TRUE.
Details
Generic parameters (parameter applied to all methods, such as resolution etc) are set in the function. Method dependent parameters (such as lag.start, lag.end for method = 'static'), are stored in profile.csv in PREF folder under extdata. To change preference parameter, can either programably or manually go to folder system.file('extdata','PREF','profile.csv',package='sojourner'), and c hange the profile.csv.
lag.start: time lag used as start of dt for compute Dcoef. Default 2. lag.end: Time lag used as end of dt for compute Dcoef. Default 2.
method for calculating Dcoef:
static stabilize the number of time lags used for fitting using time lag 2~ 5 despite the total time lags measured.
percentage 'percentage', uses (tierd) percentage (default 0.25) of time lags.
[,1] TrackLength Percentage TimeLagsForFitting [,2] 31~ 0.25 2~5-2~7 [,3] 22~30 0.25 2~5-2~7 [,4] 15~21 0.4 2~5-2~7 [,5] 10~15 0.6 2~5-2~7 [,6] 7~9 1 2~5-2~7 [,1] rolling.window time lags uses for Dcoef follows a rolling window with specified window size (default 4).
Examples
# compare files folder=system.file('extdata','SWR1',package='sojourner') trackll = createTrackll(folder=folder, input=3)#> #> Reading ParticleTracker file: SWR1_WT_140mW_image6.csv ... #> #> mage6 read and processed. #> #> Process complete.#> applying filter, min 7 max Inf #> 45 tracks length > & = 1 45 tracks length > & = 2 45 tracks length > & = 3 45 tracks length > & = 4 45 tracks length > & = 5 45 tracks length > & = 6 #> #> ...Dcoef(MSD=MSD,method='static',plot=TRUE)#> #> applying static,lag.start= 2 lag.end= 5 #> lag.start 2 lag.end 5 #> #> Applying r square filter... 0.8#> Warning: NaNs produced#> #> Plotting histogram... #> auto binwidth = 0.2613932#> Warning: Removed 3 rows containing non-finite values (stat_bin).#> #> Plotting density... #> auto binwidth = 0.2613932#> Warning: Removed 3 rows containing non-finite values (stat_bin).#> Warning: Removed 3 rows containing non-finite values (stat_density).# compare folders folder1=system.file('extdata','SWR1',package='sojourner') folder2=system.file('extdata','HTZ1',package='sojourner') trackll2=compareFolder(folders=c(folder1,folder2), input=3)#> #> Reading ParticleTracker file: SWR1_WT_140mW_image6.csv ... #> #> mage6 read and processed. #> #> Process complete. #> #> Merging of folder SWR1 complete. #> #> ... #> #> Reading ParticleTracker file: HTZ1_140mW_WT.csv ... #> #> mW_WT read and processed. #> #> Process complete. #> #> Merging of folder HTZ1 complete. #> #> ...Dcoef(trackll=trackll2,method='percentage',plot=TRUE)#> #> applying percentage, 0.25 #> applying filter, min 7 max Inf #> applying trimmer, min 1 max 31 #> calculating MSD for individual tracks... folder 1 track 1 calculating MSD for individual tracks... folder 1 track 2 calculating MSD for individual tracks... folder 1 track 3 calculating MSD for individual tracks... folder 1 track 4 calculating MSD for individual tracks... folder 1 track 5 calculating MSD for individual tracks... folder 1 track 6 calculating MSD for individual tracks... folder 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folder 2 track 30 calculating MSD for individual tracks... folder 2 track 31 calculating MSD for individual tracks... folder 2 track 32 calculating MSD for individual tracks... folder 2 track 33 calculating MSD for individual tracks... folder 2 track 34 calculating MSD for individual tracks... folder 2 track 35 calculating MSD for individual tracks... folder 2 track 36 calculating MSD for individual tracks... folder 2 track 37 calculating MSD for individual tracks... folder 2 track 38 calculating MSD for individual tracks... folder 2 track 39 calculating MSD for individual tracks... folder 2 track 40 calculating MSD for individual tracks... folder 2 track 41 calculating MSD for individual tracks... folder 2 track 42 calculating MSD for individual tracks... folder 2 track 43 calculating MSD for individual tracks... folder 2 track 44 calculating MSD for individual tracks... folder 2 track 45 calculating MSD for individual tracks... folder 2 track 46 calculating MSD for individual 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MSD for individual tracks... folder 2 track 98 calculating MSD for individual tracks... folder 2 track 99 calculating MSD for individual tracks... folder 2 track 100 calculating MSD for individual tracks... folder 2 track 101 calculating MSD for individual tracks... folder 2 track 102 calculating MSD for individual tracks... folder 2 track 103 calculating MSD for individual tracks... folder 2 track 104 calculating MSD for individual tracks... folder 2 track 105 calculating MSD for individual tracks... folder 2 track 106 calculating MSD for individual tracks... folder 2 track 107 calculating MSD for individual tracks... folder 2 track 108 calculating MSD for individual tracks... folder 2 track 109 calculating MSD for individual tracks... folder 2 track 110 calculating MSD for individual tracks... folder 2 track 111 calculating MSD for individual tracks... folder 2 track 112 calculating MSD for individual tracks... folder 2 track 113 calculating MSD for individual tracks... folder 2 track 114 calculating MSD for individual tracks... folder 2 track 115 calculating MSD for individual tracks... folder 2 track 116 calculating MSD for individual tracks... folder 2 track 117 calculating MSD for individual tracks... folder 2 track 118 calculating MSD for individual tracks... folder 2 track 119 calculating MSD for individual tracks... folder 2 track 120 calculating MSD for individual tracks... folder 2 track 121 calculating MSD for individual tracks... folder 2 track 122 #> #> Applying r square filter... 0.8#> Warning: NaNs produced#> Warning: NaNs produced#> #> Plotting histogram... #> auto binwidth = 0.4251506#> Warning: Removed 6 rows containing non-finite values (stat_bin).#> #> Plotting density... #> auto binwidth = 0.4251506#> Warning: Removed 6 rows containing non-finite values (stat_bin).#> Warning: Removed 6 rows containing non-finite values (stat_density).Dcoef(trackll=trackll2,method='rolling.window',plot=TRUE)#> #> applying rolling window... #> applying filter, min 7 max Inf #> 45 tracks length > & = 1 45 tracks length > & = 2 45 tracks length > & = 3 45 tracks length > & = 4 45 tracks length > & = 5 45 tracks length > & = 6 #> #> ... #> 122 tracks length > & = 1 122 tracks length > & = 2 122 tracks length > & = 3 122 tracks length > & = 4 122 tracks length > & = 5 122 tracks length > & = 6 #> #> ... #> [1] 1 2 3 4 #> [1] 2 3 4 5 #> [1] 3 4 5 6 #> [1] 1 2 3 4 #> [1] 2 3 4 5 #> [1] 3 4 5 6 #> #> Applying r square filter... 0.8 #> #> Applying r square filter... 0.8 #> #> Applying r square filter... 0.8 #> #> Applying r square filter... 0.8 #> #> Applying r square filter... 0.8 #> #> Applying r square filter... 0.8#> Warning: NaNs produced#> Warning: NaNs produced#> Warning: NaNs produced#> #> Plotting histogram... #> auto binwidth = 0.2921864#> Warning: Removed 13 rows containing non-finite values (stat_bin).#> Warning: Removed 13 rows containing non-finite values (stat_bin).#> Warning: Removed 13 rows containing non-finite values (stat_density).#> #> Plotting density... #> auto binwidth = 0.2921864#> Warning: Removed 13 rows containing non-finite values (stat_density).#> Warning: Removed 13 rows containing non-finite values (stat_density).
