bsocialv2: Analysis of Microbial Social Behavior in Bacterial Consortia

Description

Provides an S4 class and methods for analyzing microbial social behavior in bacterial consortia. Includes growth parameter extraction, social behavior classification (cooperators/cheaters/neutrals), diversity effect analysis, consortium assembly path finding, and stability analysis via coefficient of variation.

Author(s)

Maintainer: Juan Emilio Martinez Manjon juanemartinez999@hotmail.com

Authors:

• Maria Garcia Toledo

• Jessica Purswani

• Rocio Romero Zaliz

See Also

Useful links:

• https://github.com/Juane99/bsocialv2

• Report bugs at https://github.com/Juane99/bsocialv2/issues

Analyze Biofilm Assembly Sequences

Description

Analyze Biofilm Assembly Sequences

Usage

analyze_biofilm_sequence(.Object)

Arguments

Value

The modified bsocial object with assembly path lists in resultados_analisis$biofilm_gen_paths and resultados_analisis$biofilm_gr_paths, and plot functions in graficos.

Analyze Biofilm Assembly Sequences

Description

Builds a directed graph of possible consortium assembly paths based on strain subset relationships. Uses igraph to find shortest paths between simpler and more complex consortia.

Usage

## S4 method for signature 'bsocial'
analyze_biofilm_sequence(.Object)

Arguments

Value

The modified bsocial object with biofilm paths and plot functions.

Analyze Diversity Effect on Fitness

Description

Analyze Diversity Effect on Fitness

Usage

analyze_diversity(.Object)

Arguments

Value

The modified bsocial object with diversity boxplots in graficos and relative fitness tables in resultados_analisis (keyed by diversity level and top-k strain ranking).

Analyze Diversity Effect on Fitness

Description

Analyzes the relationship between consortium diversity (number of strains) and fitness. Compares fitness across diversity levels and identifies effects of including top-ranked strains.

Usage

## S4 method for signature 'bsocial'
analyze_diversity(.Object)

Arguments

Value

The modified bsocial object with diversity analysis in graficos and resultados_analisis.

Analyze Growth Metrics

Description

Analyze Growth Metrics

Usage

analyze_growth(.Object)

Arguments

Value

The modified bsocial object with a scatter plot stored in graficos$growth_scatter and top-10 ranking tables in resultados_analisis$best_10_ngen and resultados_analisis$best_10_gr.

Analyze Growth Metrics

Description

Creates a scatter plot of LogPhase vs NGen colored by consortium diversity, and generates top-10 tables ranked by NGen and GR.

Usage

## S4 method for signature 'bsocial'
analyze_growth(.Object)

Arguments

Value

The modified bsocial object with growth analysis in graficos and resultados_analisis.

Analyze Social Behavior (Fitness Effects)

Description

Analyze Social Behavior (Fitness Effects)

Usage

analyze_social_behavior(.Object)

Arguments

Value

The modified bsocial object with resultados_analisis$social_behavior containing fitness comparison data, boxplot objects for NGen and GR, and a success flag.

Analyze Social Behavior (Fitness Effects)

Description

Compares the fitness of each strain in consortia vs its monoculture baseline. Generates boxplots showing relative fitness for each strain across all consortia.

Usage

## S4 method for signature 'bsocial'
analyze_social_behavior(.Object)

Arguments

Value

The modified bsocial object with resultados_analisis$social_behavior.

Analyze Consortium Stability

Description

Analyze Consortium Stability

Usage

analyze_stability(.Object)

Arguments

Value

The modified bsocial object with coefficient of variation data in resultados_analisis$stability_cv_data and violin plots in graficos$stability_ngen_plot and graficos$stability_gr_plot.

Analyze Consortium Stability

Description

Calculates the coefficient of variation (CV) for growth metrics across replicates or diversity levels. Creates violin plots with Spearman correlation, p-value, and R-squared displayed as subtitles.

Usage

## S4 method for signature 'bsocial'
analyze_stability(.Object)

Arguments

Value

The modified bsocial object with stability analysis results.

S4 Class for Microbial Social Behavior Analysis

Description

The bsocial class encapsulates data and results for analyzing microbial social behavior in bacterial consortia.

Slots

id_proyecto

Character. Project identifier.

cepas_seleccionadas

Character vector. Names of the selected strains.

datos_crudos

List. Raw input data (plates, curated, consortia).

datos_procesados

Data frame. Processed metrics (NGen, GR, LogPhase).

resultados_analisis

List. Analysis results from each pipeline step.

graficos

List. Generated ggplot2 plots and plotting functions.

Examples

obj <- new("bsocial")
obj@id_proyecto <- "my_experiment"

Log Messages for bsocialv2 Operations

Description

Internal logging utility that outputs timestamped messages to the console.

Usage

bsocial_log(level = "INFO", ..., .indent = 0)

Arguments

Value

NULL (invisibly). Called for its side effect of printing a message.

Calculate Growth Parameters from Preprocessed Curves

Description

Calculate Growth Parameters from Preprocessed Curves

Usage

calculate_growth_params(.Object, ...)

Arguments

Value

The modified bsocial object with datos_procesados populated as a data frame containing consortia identifiers, strain presence/absence, and growth parameters (LogPhase, NGen, GR) fitted from the preprocessed curves.

Calculate Growth Parameters from Preprocessed Curves

Description

Fits growth curves and extracts LogPhase, number of generations (NGen), and growth rate (GR) for each consortium.

Usage

## S4 method for signature 'bsocial'
calculate_growth_params(.Object, method = "growthcurver")

Arguments

Value

The modified bsocial object with datos_procesados populated.

Plot Preprocessed Growth Curves

Description

Plot Preprocessed Growth Curves

Usage

plot_processed_curves(.Object)

Arguments

Value

A ggplot object showing faceted line plots of mean growth curves (optical density over time) grouped by experimental condition.

Plot Preprocessed Growth Curves

Description

Creates a faceted line plot of mean growth curves after preprocessing, grouped by experimental condition.

Usage

## S4 method for signature 'bsocial'
plot_processed_curves(.Object)

Arguments

Value

A ggplot2 object.

Classify Strains as Cooperators, Cheaters, or Neutrals

Description

Classify Strains as Cooperators, Cheaters, or Neutrals

Usage

summarize_social_behavior(.Object, ...)

Arguments

Value

The modified bsocial object with resultados_analisis$summary_gen and resultados_analisis$summary_gr, each a list with character vectors positives (cooperators), negatives (cheaters), and neutrals.

Classify Strains as Cooperators, Cheaters, or Neutrals

Description

Uses pairwise t-tests and median comparisons to classify each strain based on its effect on consortium fitness.

Usage

## S4 method for signature 'bsocial'
summarize_social_behavior(.Object)

Arguments

Value

The modified bsocial object with resultados_analisis$summary_gen and $summary_gr.

Import Pre-processed (Curated) Data

Description

Import Pre-processed (Curated) Data

Usage

transform_curated_data(.Object, ...)

Arguments

Value

The modified bsocial object with datos_procesados populated as a data frame containing consortia identifiers, strain presence/absence, and growth parameters (LogPhase, NGen, GR).

Import Pre-processed (Curated) Data

Description

Imports a pre-processed CSV containing growth parameters already calculated externally. Expected columns: Consortia, LogPhase, NGen, GR, plus strain presence/absence columns matching cepas_seleccionadas.

Usage

## S4 method for signature 'bsocial'
transform_curated_data(.Object)

Arguments

Value

The modified bsocial object with datos_procesados populated.

Preprocess Raw Plate Reader Data

Description

Preprocess Raw Plate Reader Data

Usage

transform_raw_data(.Object, ...)

Arguments

Value

The modified bsocial object with resultados_analisis populated with preprocessed growth curves, cycle times, curve mapping, and replicate statistics.

Preprocess Raw Plate Reader Data

Description

Normalizes raw plate reader data by applying background correction and aggregating replicates. Supports blank-based or OD threshold correction.

Usage

## S4 method for signature 'bsocial'
transform_raw_data(.Object, groups, bg_type, bg_param)

Arguments

Value

The modified bsocial object with resultados_analisis populated.