ecoli.analysis.antibiotics_colony.validation

ecoli.analysis.antibiotics_colony.validation.plot_colony_growth(data, ax=None, axs=None, antibiotic='Tet.', antibiotic_col='Initial external tet.', mic=3.375)[source]

Plot traces of total colony mass and total colony growth rate. Can use methodology described in Lambert and Pearson 2000 to empirically calculate MIC from simulated data if a list of two axes is provided using axs

Parameters:

  • data (pandas.DataFrame) – DataFrame where each row is an agent and each column is a variable of interest. Must have these columns: ‘Time’, ‘Condition’, and ‘Dry Mass’. The first experimental condition in the ‘Condition’ column is treated as a control (default gray). Include at most 2 conditions and 1 seed per condition.

  • ax (Axes | None) – List of 2 Matplotlib Axes, one for colony mass and other for MIC

  • axs (List[Axes] | None) – List of 2 Matplotlib Axes, one for colony mass and other for MIC

  • antibiotic (str) – Name of antibiotic to put as legend title

  • antibiotic_col (str) – Name of column with initial external antibiotic concs.

  • mic (float) – Minimum inhibitory concentration (uM, rounded to 3 decimal places)

Return type:

None

ecoli.analysis.antibiotics_colony.validation.plot_death_timescale_analysis(data, axs, antibiotic_col='Initial external amp.', mic=5.724)[source]

Create histogram of cell age (time since birth) until death and labelled scatterplot of average time exposed to ampicillin until death against initial external ampicillin concentration.

Parameters:

  • data (pandas.DataFrame) – DataFrame where each row is an agent and each column is a variable of interest.

  • axes – List of 2 matplotlib Axes instances on which to draw plots

  • antibiotic_col (str) – Name of column with initial external antibiotic concs.

  • mic (float) – Minimum inhibitory concentration (uM, rounded to 3 decimal places)

  • axs (List[Axes])

ecoli.analysis.antibiotics_colony.validation.plot_mass_fraction(data)[source]

Plot line plots of submass fold changes over generation time.

Parameters:

data (pandas.DataFrame) – DataFrame where each row is an agent and each column is a variable of interest.

ecoli.analysis.antibiotics_colony.validation.plot_mrna_fc(data, ax, genes_to_plot, highlight_genes=None)[source]

Plot scatter plot of simulated and experimental log2 fold change for final mRNA concentrations of key genes regulated during tetracycline exposure.

Parameters:

  • data (pandas.DataFrame) – DataFrame where each row is an agent and each column is a variable of interest. Must have these columns: ‘Time’, ‘Condition’, and ‘Dry Mass’. The first experimental condition in the ‘Condition’ column is treated as a control.

  • ax (Axes) – Single instance of Matplotlib Axes to plot on.

  • genes_to_plot (list[str]) – List of gene names to include in plot.

  • highlight_genes (dict[str, tuple] | None) – Mapping of gene names to point colors.

Return type:

None

ecoli.analysis.antibiotics_colony.validation.plot_protein_synth_inhib(data, ax, literature)[source]

Plot scatter plot of normalized % protein synthesis inhibition across a variety of tetracycline concentrations.

Parameters:

  • data (pandas.DataFrame) – DataFrame where each row is an agent and each column is a variable of interest. Must have these columns: ‘Time’, ‘Condition’, ‘Seed’, and ‘Dry Mass’.

  • ax (Axes) – Single instance of Matplotlib Axes to plot on.

  • literature (pandas.DataFrame) – DataFrames with 3 columns: ‘Tetracycline’, ‘Percent inhibition’, and ‘Source’