ecoli.analysis.antibiotics_colony.plot

Script to make majority of figures in paper. Before running, extract colony_data.zip in the “data” folder. Mapping between filenames in “colony_data/sim_dfs” folder and simulation conditions in ecoli/analysis/antibiotics_colony/__init__.py. The __init__ file also constructs a dictionary of all columns in the saved CSV files (and gives their paths in the simulation store hierarchy).

Refer to these other scripts for the code to create remaining figures:
  • ecoli/analysis/antibiotics_colony/subgen_gene_plots/
    • count_subgen.py: counts for Fig. 1B
      • Run with “–data data/colony_data/glc_10000_expressome.csv”

    • make_fig_1b.py: create Fig. 1B

  • ecoli/analysis/antibiotics_colony/snapshot_and_hist_plot.py: Fig. 2E-F
    • Run with “–local data/colony_data/2022-12-08_00-35-28_562633+0000.csv”

  • ecoli/analysis/antibiotics_colony/tet_dry_mass.py: Fig. 3E

  • ecoli/analysis/antibiotics_colony/amp_plots.py: Fig. 4D-J, L
    • Run with “–glc_data data/colony_data/2022-12-08_00-33-56_581605+0000.csv” and “–amp_data data/colony_data/2022-12-08_17-03-56_357734+0000.csv”

  • ecoli/analysis/antibiotics_colony/spatial_autocorrelation.py: Fig. S4
    • Run with “data/colony_data/sim_dfs/2022-12-08_00-35-28_562633+0000.csv”

    • Repeat with CSV files for other two baseline glucose simulations to get all Moran’s I and p-values in Table S1

  • ecoli/analysis/proteinCountsValidation.py: Fig. S2A
    • Run with “–avg_data data/colony_data/glc_10000_proteome_avgs.csv”

  • ecoli/analysis/centralCarbonMetabolismScatter.py: Fig. S2B
    • Run with “–numpy_data data/colony_data/glc_10000_fluxome.csv” and “–sim_df data/colony_data/2022-12-08_00-35-28_562633+0000.csv”

ecoli.analysis.antibiotics_colony.plot.load_exp_data(experiment_ids)[source]
ecoli.analysis.antibiotics_colony.plot.main()[source]
ecoli.analysis.antibiotics_colony.plot.make_figure_1a(data, metadata)[source]
ecoli.analysis.antibiotics_colony.plot.make_figure_2a(data, metadata)[source]
ecoli.analysis.antibiotics_colony.plot.make_figure_2b_d(data, metadata)[source]
ecoli.analysis.antibiotics_colony.plot.make_figure_3d_and_3m(data, metadata)[source]
ecoli.analysis.antibiotics_colony.plot.make_figure_3f_h(data, metadata)[source]
ecoli.analysis.antibiotics_colony.plot.make_figure_3i_k(data, metadata)[source]
ecoli.analysis.antibiotics_colony.plot.make_figure_3l(data, metadata)[source]
ecoli.analysis.antibiotics_colony.plot.make_figure_4c(data, metadata)[source]
ecoli.analysis.antibiotics_colony.plot.make_figure_4l(data, metadata)[source]
ecoli.analysis.antibiotics_colony.plot.make_figure_4m(data, metadata)[source]
ecoli.analysis.antibiotics_colony.plot.make_figure_4n(data, metadata)[source]
ecoli.analysis.antibiotics_colony.plot.make_figure_s1(data, metadata)[source]
ecoli.analysis.antibiotics_colony.plot.make_figure_s10(data, metadata)[source]
ecoli.analysis.antibiotics_colony.plot.make_figure_s3a(data, metadata)[source]
ecoli.analysis.antibiotics_colony.plot.make_figure_s3b(data, metadata)[source]
ecoli.analysis.antibiotics_colony.plot.make_figure_s5(data, metadata)[source]
ecoli.analysis.antibiotics_colony.plot.make_figure_s6a(data, metadata)[source]
ecoli.analysis.antibiotics_colony.plot.make_figure_s6b(data, metadata)[source]
ecoli.analysis.antibiotics_colony.plot.make_figure_s7(data, metadata)[source]
ecoli.analysis.antibiotics_colony.plot.make_figure_s8(data, metadata)[source]
ecoli.analysis.antibiotics_colony.plot.make_figure_videos(data, metadata)[source]

One-off video of sub-generational ampC expression and cell death at MIC.

Parameters: