Output Plots

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

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Plot Format

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

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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
)

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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)

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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