whiB7KO screen (2023)

Repository containing the code and methods for Poulton et al. 2023

Below is a short legend describing the main files, followed by example running the code:

vulnerability_modeling_tools.R

R code with functions useful for running the vulnerability analysis.

vulnerability_plotting_tools.R

R code with functions useful for plotting vulnerability results

gene_vulnerability_analysis.R

R code for running vulnerability analysis in paralell.

model_negbinom_2line_logistic_w_guide_lambda_betamin_zero.stan

Stan code for the vulnerability model.

gene_vulnerability_plots.R

R code for creating plots of vulnerability results in parallel.

Example

Analysis

Users can run the vulnerability analyis performed in the paper using the following script:

gene_vulnerability_analysis.R

The following parameters must be passed:

• data: path to dataframe containing the counts data
• strain: strain of the organism (for tracking/labeling purposes)
• label: short label (for tracking/labeling purposes)
• output: output directory for the samples and model data for each gene
• cores: number of cores to run in parallel

Example:

Rscript gene_vulnerability_analysis.R --data data/data_counts_atc_Smeg_whiB7KO_08_10_2023.txt --strain Smeg --label Smeg_whiB7KO --output results/ --cores 40

Plotting

Similarly, users can create plots of the results by running the following script:

gene_vulnerability_plots.R

Users can provide four parameters:

• data: path to dataframe containing the counts data
• strain: strain of the organism (for tracking/labeling purposes)
• exp: short label for the experiment (for tracking/labeling purposes)
• date: date where the run, experiments, or processing were done (for tracking/labeling purposes)
• plot_dir: output directory for the plots
• dir: directory where the samples and model data were outputed by the sampling process
• cores: number of cores to run in parallel

Example:

Rscript gene_vulnerability_plots.R --data data/data_counts_atc_Smeg_whiB7KO_08_10_2023.txt --strain Smeg --exp whiB7KO --date 08_10_2023 --plot_dir plots/ --dir results/ --cores 10