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Output - Plots

This page describes the plots output folder generated by SigProfilerMatrixGenerator.

Overview

When plot=True is set, SigProfilerMatrixGenerator integrates with SigProfilerPlotting to generate visualizations for all matrix types.

Generated Plots

Standard Plots

Plot Type Description
SBS-6 6-channel single base substitution barplot
SBS-24 24-channel SBS with strand bias
SBS-96 Standard 96-channel mutational signature plot
SBS-384 Extended SBS with strand bias
DBS-78 78-channel double base substitution plot
DBS-186 Extended DBS with strand bias
ID-28 Basic indel classification plot
ID-83 Extended indel classification plot
ID-415 Indel with strand bias plot

Additional Plots (Available via SigProfilerPlotting)

Plot Type Description
SBS-1536 Extended context SBS plot
Sample portrait Comprehensive sample summary

Plot Format

  • File format: PDF (multi-page)
  • Content: One page per sample
  • Naming: [project]_[matrix_type].pdf

Enabling Plot Generation

To generate plots, set plot=True:

from SigProfilerMatrixGenerator.scripts import SigProfilerMatrixGeneratorFunc as matGen

matrices = matGen.SigProfilerMatrixGeneratorFunc(
    "my_project",
    "GRCh37",
    "/path/to/input",
    plot=True
)

Plot Examples

SBS-96 Plot

The standard 96-channel plot shows: - X-axis: 96 trinucleotide contexts grouped by mutation type - Y-axis: Mutation count or frequency - Colors: Different colors for each of the 6 mutation types - C>A (blue) - C>G (black) - C>T (red) - T>A (gray) - T>C (green) - T>G (pink)

ID-83 Plot

The indel plot shows: - 1bp C deletions (orange) - 1bp T deletions (orange, lighter) - 1bp C insertions (green) - 1bp T insertions (green, lighter) - Long deletions at repeats (pink) - Long insertions at repeats (light pink) - Microhomology deletions (brown)

SigProfilerPlotting

For more advanced plotting options and customization, use SigProfilerPlotting directly:

GitHub: https://github.com/AlexandrovLab/SigProfilerPlotting

Installation: 

pip install sigProfilerPlotting

Features: - Custom color schemes - Publication-quality figures - Additional plot types - Sample comparison plots - Signature decomposition visualizations