Project 3: V-Plot Matrix Generator

Goal: Visualize the relationship between DNA fragment size and genomic position. This tool generates a "Long Form" matrix from raw sequencing data (BED format) and visualizes the fragment length distribution as a heatmap. It is designed to handle massive genomic datasets by streaming data and using memory-efficient plotting techniques.

File Structure

File	Language	Description
vplot_matrix.py	Python	Reads piped BED data, calculates fragment centers/lengths, and outputs a long-form matrix.
vplot_graph.R	R	Reads the matrix and generates a heatmap using ggplot2. Includes auto-scaling for genomic coordinates.

Prerequisites

• Python 3
• R (Libraries: ggplot2)
• Standard tools: zcat

Usage

1. Generate the Matrix & Plot

Run the entire pipeline in a single command using pipes. This example uses shuf.a.bed.gz as the input.

zcat shuf.a.bed.gz | python vplot_matrix.py > matrix_long_form.tsv && Rscript vplot_graph.R

Output files

matrix_long_form.tsv vplot_result.png