Plotting

This module provides a comprehensive set of tools for visualizing data and results from ODE-based models of phosphorylation dynamics. It supports various types of plots to analyze model behavior, parameter estimates, and goodness-of-fit metrics.

Features

• Time-Series Visualization:
  Generate plots for time-dependent data, including mRNA, protein, and phosphorylation levels.

• Dimensionality Reduction:
  Visualize data using PCA, t-SNE, and parallel coordinates to explore patterns and relationships.

• Parameter Analysis:
  Create scatter plots, bar charts, and density plots to evaluate parameter estimates, confidence intervals, and sensitivity.

• Model Fit Evaluation:
  Compare observed and fitted data using goodness-of-fit plots, error distributions, and Kullback-Leibler divergence.

• Sensitivity Analysis:
  Visualize parameter importance and interactions using bar plots, scatter plots, radial plots, and pie charts.

• State and Phase Space Exploration:
  Analyze state variability over time and phase space relationships between states.

• Regularization and Error Metrics:
  Summarize regularization values and model errors across genes or experiments.

Output

All plots are saved as high-resolution images in the specified output directory.
Interactive visualizations (e.g., Plotly) are also supported for model fit only.