link{createFrequencyMatrix}. It places a particular emphasis
on identifying paralysis and quantifying the kinetic elements of paralysis
during swimming.
expfile is the path of the frequency matrix returned by the
link{createFrequencyMatrix} function.
annfile is the path of annotation file returned by the
link{createFrequencyMatrix} function.
projectname is the name of the project.
outputPath is a directory which saves the plots and files returned
by the function.
color is "red/green".
data.collection.interval is the time interval between two points
and the default is 0.067.
window.size is the size of the window for the running average
that is calculated to smooth the data. The default is 150.
mads is the number of median absolute deviations that a given animal
must deviate from the median sum of frequencies to be called an outlier.
The default is 4.4478.
quantile is the proportion of data points that are used in calculating
the color scheme for the heat map and the default is 0.95.
interval is the minimum time that a given animal must lie below a threshold
to be called a paralyzed worm for the first calculation and the default is 20.
degree is the paralytic degree for the first calculation and
the default is 0.2.
paralysis.interval is the same as interval but for the second
calculation and the default is 20.
paralysis.degree is the paralytic degree for the second calculation
and the default is 0.2.
rev.degree is the threshold that an animal must cross to be called
a revertant and the default is 0.5.
sample_t_half contains each animal and their corresponding latency to paralyze.
For non-paralyzers, N/A will be listed.
group_data is defined as follow.
"freq_max_mean": Mean maximal swimming frequency;
"freq_max_sd": Standard deviation of Mean maximal swimming frequency;
"freq_min_mean": Mean minimum swimming frequency;
"freq_min_sd": Standard deviation of Mean minimum swimming frequency;
"freq_range_mean": Mean range between maximum and minimum;
"freq_range_sd": Standard deviation of Mean range between maximum and minimum;
"paralytic_count": The number of paralyzed animals amongst the samples;
"non-paralytic_count": The number of non-paralyzed animals amongst the samples;
"t_half_mean": Mean latency to cross the paralytic threshold set by the users
(default is 20
interval (default is 20 seconds);
"t_half_sd": Standard deviation of t_half_mean;
"t_p_start_mean": The mean time point (in seconds) at which each animal crosses
a frequency that is min+paralytic threshold and stays below that threshold for
the paralytic interval;
"t_p_start_sd": Standard deviation of t_p_start_mean;
"t_p2end_mean": The average range of time after paralysis;
"t_p2end_sd": Standard deviation of t_p2end_mean;
"rev_count": The number of revertants amongst the samples as defined by
the threshold set by the user (default is animals have to recross 50
frequency range for any length of time;
"rev_percent": The number of revertants;
"rev_frequency_mean": The number of reversion events;
"t_p2r_mean": Mean time between 1st reversion and t_p_start_mean;
"t_p2r_sd": Standard deviation of t_p2r_mean;
"t_r_total_mean": Mean of total time spent in reversion for all revertants;
"t_r_total_sd": Standard deviation of t_r_total_mean;
"t_r_average_mean": Mean length of an individual reversion event;
"t_r_average_sd": Standard deviation of t_r_average_mean;
"r_amp_mean": Mean of total amplitude of reversion for all revertants,
where amplitude is defined by the area beyond the reversion threshold set
by user (default is 50
discrete values for each measurement (same unit as frequency);
"r_amp_sd": Standard deviation of r_amp_mean.
group.ordered.data contains the data after outlier exclusion, smoothing and
ordering based on the latency to paralyze.
individual.data contains reversion information for individual animals.
The definitions are identical to the group_data, but "R_count" is the number of
reversion events for that animal. If there is no paralyzed animal, it will not be returned.
group_means contains average frequency and standard deviation for each group.
The row names are the time.
nooutliers.smoothed.data is a list object which contains all frequency data
points broken up into increasing 0.1 Hz bins after exclusion and smoothing for each of genotypes.
output_SwimR.html contains a summary of all output files. 2. P_sample_t_half.txt is a TXT file which contains the information of sample_t_half.
"P" of "P_sample_t_half.txt" is the projectname inputted by users.
3. P_group_data.txt is a TXT file which contains the information of group_data.
4. P_heatmap_withingroup_ordered_globalcentering.jpg is a JPEG file of the
heat map of all of the samples included in the data matrix after outlier exclusion,
smoothing, ordering based on the latency to paralyse, and centering the color
based on the quantile percent that can be set by the user in the parameters section
of SwimR.
5. P_heatmap_withingroup_ordered.txt is a TXT file of the raw data used to plot the heat map
which is the same with group.ordered.data.
6. After exclusion and smoothing, P_histogram.nooutliers.smoothed.jpg
is a JPEG file of all frequency data points broken up into increasing 0.1 Hz
bins and then plotted as the fraction of the total as a histogram.
7. P_histogram.nooutliers.smoothed.data.G.txt is a TXT file of
the raw data used to plot the histogram, which is the same with nooutliers.smoothed.data.
"G" in the "P_histogram.nooutliers.smoothed.data.G.txt" is the genotype in the annotation file.
8. P_individual_data.txt is a TXT file which contains the information of individual.data.
If there is no paralyzed animal, this file will not be outputted.
9. P_individual_data1.txt is a TXT file which contains the information of individual.data1.
If there is no paralyzed animal, this file will not be outputted.
10. P_intermediate.results.txt describes some key features of your
samples after running SwimR, and is a great way to get a quick look at the
incidence of paralysis amongst your samples. At the top of the file, it lists
the parameters used in the subsequent calculations. Below that, it lists the
summed frequency values for each of the animals included in the sample. And
then the p value of the bimodal test for each genotype was listed. Below that,
it lists each of the animals included and excluded after outlier detection.
After that, it lists which animals were considered paralyzed and which not.
For paralyzed animals, it then lists which of them were called revertants.
11. P_scatter.jpg is a JPEG image of the average frequency plotted
against time after outlier exclusion, but w/o smoothing.
12. P_nooutliers_smoothed_scatter.jpg is a JPEG image of the average
frequency plotted against time after outlier exclusion and smoothing.
13. P_nooutliers_smoothed_scatter_data.txt is a TXT file of the raw data
used to plot the smoothed scatter.pdf, which is the same with group_means.
createFrequencyMatrix
expfile <- system.file("extdata", "SwimExample", "SwimR_Matrix.txt", package="SwimR")
annfile <- system.file("extdata", "SwimExample", "SwimR_anno.txt", package="SwimR")
projectname <- "SwimR"
outputPath <- getwd()
result <- SwimR(expfile, annfile, projectname, outputPath, color = "red/green",
data.collection.interval = 0.067, window.size = 150, mads = 4.4478, quantile = 0.95,
interval = 20, degree = 0.2, paralysis.interval = 20, paralysis.degree = 0.2,
rev.degree = 0.5)
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