scripts and raw data for analysis of long chain fatty acid fitness scores, relative to a glucose control. Functions from the sister repository fitness_score/ are a prerequisite for these scripts.
Dependencies
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MATLAB 2014a or later recommended
Requires the MATLAB scripts from fitness_score/ (https://github.com/AnthonyShiverMicrobes/fitness_score)
Running the code
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First, load the keio6index. This index specifies how to approach the keio6 plate for normalization. The keio6index is found within pathtorepository/metadata/keio6index.mat
Second, open up the script automated_oleate_sizer.m and enter the full path to the data directory in this repository on your local clone. This will look something like parent='/Users/brucewayne/Documents/MATLAB/fitness_lcfa/data/'.
Third, make sure that both repositories fitness_lcfa/ and fitness_score/, as well as all subfolders, have been added to the MATLAB path.
Finally, run the script automated_lcfa_assembly.m
Looking at the raw data
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Colony sizes and metadata that were used for analysis are stored in data/ and metadata/ respectively.
--Folders--
batchanalysis/
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automated_lcfa_assembly.m calls the scoring, stitching, and filtering/normalization steps to generate a final dataset as published.
It outputs oleateS and oleateM for the scores and metadata of the screen, respectively.
driver_scripts/
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scoreLCFA.m generates normalized scores for a single plate, using the functions generated specifically for the analysis of growth on carbon sources relative to a glucose control.
data/
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The raw data used in analysis can be found in data/
KEIO-key plates are recreated from Shiver et al. 2016. The plate data from RC-phen-sizer are taken from the raw data of Nichols et al. 2010.
normalization/ score/ and stitch/
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These folders contain the functions written to specifically analyze the growth on carbon sources relative to a glucose control. Functions are organized among folders according to general purpose.