Track analysis workflow:

Track input

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:

Select and binarise the light protocol from a csv file

to do: automate threshold

Script 0.2:

Data processing 1 - global

Garnish 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:

Data processing 2 - quadrant protocol

Calculate PI (by fly and by repeat)

Script 2.1:

Data processing 3 - section3 protocol

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)

Extract 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:

Collapse stats to 1s bins

to do: look at median and standard deviation too

Script 3.3

Figure design

try to work out what this is good for, if anything

show plot of PCA for a laugh

Script 3.4

Data processing 4: Virtual quadrant design

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 an arena list, or I can pull out its definition) to simplify track assembly by rotating things about instead of shifting

to do: decide/try either chunking by classifier or going entirely blindly.

Data processing 5: Classifier

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

PaolaCognigni/CTraxHelper documentation built on May 7, 2019, 11:57 p.m.