inputPath is a directory which contains the files returned by
the Tracker program. Because annotation file is generated by extracting
the genotype information from tracker file names, the user should use dashes
to denote genotypes and separate the date in the file name like
Genotype_Drug(if used)_Dose(if used)_Date_#. The following are some examples
of tracker file names: N4_AMPH_100uM_2-11-14_1 (genotype is N4),
dat-1ok157_IMI_10uM_12-12-12_7(genotype is dat-1ok157),
cat-2e1112dat-1ok157_2-20-09_2 (genotype is cat-2e1112dat-1ok157)
and dat-1ok157dop-3vs106_5-17-06_4 (genotype is dat-1ok157dop-3vs106).
outputPath is a directory which saves the plots and
files returned by the function.
method is "Extrema".
Threshold is the amount of degrees (in radians) required
to count at as thrash and the default is 0.6.
DeltaPeakDt is the threshold for "peak delta" algorithm,
similar to Threshold and the default is 1.6.
MinFrameBtwnMax is the minimum number of frames
between maxima and the default is 4.
MinDelta is similar to DeltaPeakDet
and the default is 2.5.
longPeriod is the longest period cycle which is not zerod
and the default is 5.
AvWindowSize is the length of the average window in seconds
and the default is 10 seconds.
fps is the frame per second and the default is 15.
ZP_Length is the Zero-padding length and the default is 100.
WindowSize is the size of window for computing the Fast Fourier Transform
and the default is 30.
MaxCompWin is the window size on deciding if the current angle is a maxima
and the default is 2.
minTime is the minimum threshold of time points for the following analysis
and the default is 0 second.
maxTime is the maximum threshold of time points for the following analysis
and the default is 600 seconds.
frequencyMatrix combines the analysis results
of the frequency of worm thrashing over time for all Tracker files in the inputPath.
annotation contains all genotype information extracted
from file names of all Tracker files in the inputPath.
outputDescription_createFrequencyMatrix.html contains a summary of
all output files. 2. XFig.jpg is the image of scatter plot of one animal plotted as
"Frequency vs Time(min)" with all four counting methods overlaid.
"X" of "XFig.jpg" represents the input file names.
3. XFigSub.jpg is the same as XFig.jpg except counting methods
are broken up into four different plots. This is very helpful in checking through
a video to make sure that Tracker tracked the worm properly. Bad contrast can be
a problem with Tracker missing the worm and these files help to identify troublesome
videos for retracking or discarding.
4. XFreq.csv is the CSV file of raw data organized by column,
where column one represents frequency as counted by FFT, column two represents
frequency calculated by Extrema, column three represents frequency calculated by
PeakDt, column four represents frequency as counted by RT+GP and column five
represents time in seconds.
5. frequencyMatrix.txt is a TXT file which contains the information of frequencyMatrix.
6. annotationfile.txt is a TXT file which contains the information of annotation.
SwimR
inputPath <- system.file("extdata","trackerFiles",package="SwimR")
outputPath <- getwd()
freMat <- createFrequencyMatrix(inputPath, outputPath, method = "Extrema",
Threshold = 0.6, DeltaPeakDt = 1.6, MinFrameBtwnMax = 4, MinDelta = 2.5, longPeriod = 5,
AvWindowSize = 10, fps = 15, ZP_Length = 100, WindowSize = 30, MaxCompWin = 2, minTime = 0,
maxTime = 600)
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