spiralChronogram 1.3.0

A package to generate various types of 2D representations of data and spiral chronograms.

Chronogram Plotting Package

This package provides a function to plot a chronogram (triangular or spiral) based on a distance matrix and corresponding dates. The main function, plot_chronogram, generates these plots with customizable parameters. Here are some sample outputs generated using NCBI Virus SARS-CoV-2 Data.

Triangular Chronogram	Spiral Chronogram

Description

The main.py function plots a chronogram (triangular or spiral) based on the provided distance matrix and dates.

Parameters

• distance_matrix_path (str): Path to the distance matrix file.
• dates_file_path (str): Path to the dates file.
• threshold (int, default=1000): Threshold for the spiral, number of date units in each circle.
• pattern (str, default='nonoverlap'): Pattern indicating overlap or non-overlap if spiral has more than one circle.
• transform (bool, default=False): Whether to apply log transformation to angles.
• aggregate_data (bool, default=False): Whether to aggregate the data before plotting.
• gap (int, default=100): Gap between circles for the spiral.
• color (str, default='Spectral'): Color map for the plot.
• plot_type (str, default='spiral'): Type of chronogram to plot ('triangular', 'spiral', 'upper_triangle', 'spiral_3d').
• date_type (str, default='D'): Unit of the dates ("D": days, "M": months, "Y": years).
• tick_step (int, default=100): The increment of highlight tick.
• plot_title (str, default = None): The plot title.

Installation

1. Download the repository as a ZIP file from GitHub: https://github.com/thushari93/Spiral_Chronogram

2. Extract the ZIP file.

3. Navigate to the extracted folder:

cd <path-to-extracted-folder>

5. Install the necessary dependencies:

pip install -r requirements.txt

Example Usage

Command to compute distance matrix and extract collection dates:

python process_sequences.py --input_pattern "data_*.csv" --aligned_sequence_file "aligned_sequences.fasta"

Command to generate the plot under default settings:

python main.py --distance_matrix_path <path> --dates_file_path  <path> 

Command to generate a customized plot:

python main.py --distance_matrix_path 'distance_matrix_FL.npy' --dates_file_path  'Dates_FL.csv'
--plot_type 'spiral' --aggregate_data --transform --threshold 600 

Contributing

Feel free to submit issues to [e-mail], fork the repository, and send pull requests!

Aknowledgement

This project was funded by Institute for Mathematical and Statistical innovation (IMSI) and the University of Illinois Urbana-Champaign (UIUC) under the supervision of Dr. Wilson and Dr. Ho.

License

This project is licensed under the Creative Commons License.