Select and upload CTrax files into R objects
to do: define a
trx
class for the data frame and some wrapper class for the experiment list
Script 0.1:
raw
listSelect and binarise the light protocol from a csv file
to do: automate threshold
Script 0.2:
t
time protocol data frameGarnish data combining time protocol information
to do: impose correct var type (factor, int, num) to variables
to maybe do: add some vars (log transforms and abs), think of more?
Script 1.1:
raw
and t
garn
listCalculate PI (by fly and by repeat)
Script 2.1:
garn
PIfly
and PIrept
(PIbyfly
and PIbyrept
too?)Tidy section 3 time protocol
generalise to a given known protocol (frames on, frames repeat)
add drift?
Script 3.1: (note: there is no reason not to run this immediately after 0)
t
and protocol parameterstsynth
data frame and perhaps the progress
time annotatorExtract section 3 to produce a subsetted data frame of all genotypes
to do: once the exp class is defined, create a listtodf method
to do: think more seriously about the structure of
tsynth
(esp the strange chunk 3 declaration)
Script 3.2:
raw
or garn
and tsynth
s3df
Collapse stats to 1s bins
to do: look at median and standard deviation too
Script 3.3
s3df
s3mean
(and possibly s3median
and s2df
)Figure design
try to work out what this is good for, if anything
show plot of PCA for a laugh
Script 3.4
s3df
s3figs
Generate synthetic fly paths by fragmenting and collating on and off real paths
idea: define x and y in radial coords from the centre of the plate (somewhere in
garn
there may still be anarena
list, or I can pull out its definition) to simplify track assembly by rotating things about instead of shiftingto do: decide/try either chunking by classifier or going entirely blindly.
Describe fly behaviour by its vars
pick up old classifier again
try unsupervised, with new vars (spin, possibly friends)
look into markov chain analysis of behavioural transitions
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