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Analysis and Figures for AMiGA Manuscript

AMiGA: Software for Automated Analysis of Mirobial Growth Assays FS Midani, J Collins, and RA Britton. bioRxiv (2020).

The ./amiga/examples/manuscript/ folder houses all of the data and code needed to generate the fgures for the manuscript. To re-run the analysis and generate the figures on your machine, please do the following:

(1) Make sure that AMiGA is installed and runs successfully on your machine. See Installation for instructions and requirements.

(2) Change directory into./amiga/examples/manuscript/

(3) In your shell terminal, define variables for (i) file path that activates your python virtual environment and (ii) your current installation of AMiGA. For example,

venv=/Users/firasmidani/rab_fm/envs/python/AMIGA/bin/activate
amiga=/Users/firasmidani/rab_fm/git/amiga

(4) Using your terminal, execute the analysis by passing the above variables to the main driver script for analyzing data.

sh ./scripts_analysis/main.sh $venv $amiga

This step will take more than 60 minutes and may depend on the speed/memory of your machine. You can speed the up analysis by increasing the time step size using the -tss argument or reducing the number of permutations for hypothesis testing. See Command Line Interface for more details; however, keep in mind that increasing the time step size will affect estimates of growth parameters because you are reducing the input or number of time points used by model. To increase the time step size, you can edit the commands in the scripts directly. For example, adjust the -tss arguments in lines 8, 25, and 32 of analyze_death_experiment.sh and lines 66, 99, 126, and 190 in analyze_non_c_diff_expamples.sh. To adjust the number of test permutations, you only need to adjust the -np argument in line 23 of test_death_experiment_hypotheses.sh.

(5) Using your terminal, excute the figure generation by passing the above variables to the main driver script for figure generation. Figures will be automatically saved as PDFs in ./amiga/examples/manuscript/figures folder.

sh ./scripts_figures/main.sh $venv $amiga