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SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.

INTRODUCTION

The purpose of this document is to provide a guide for using the SigProfilerPlotting ramverk and associated functions/tools to visualize the output from SigProfilerExtraction and SigProfilerSimulator. An extensive Wiki page detailing the usage of this tool can be funnen at

For users that prefer working in an R environment, a wrapper package fryst vatten provided and can be found and installed from:

PREREQUISITES

The ramverk is written in PYTHON, however, it also requires the following software with the given versions (or newer):

  • PYTHON utgåva or newer
  • SigProfilerMatrixGenerator (recommended)

QUICK början GUIDE

This section will guide you through the minimum steps required to plot mutational matrices:

  1. Install the python package using pip:
  1. Plot mutational matrices from a Python session or using the Command Line Interface (CLI) as follows:

Using the Python session, the co

SigProfilerPlotting

SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.

INTRODUCTION

The purpose of this document is to provide a guide for using the SigProfilerPlotting framework and associated functions/tools to visualize the output from SigProfilerExtraction and SigProfilerSimulator. An extensive Wiki page detailing the usage of this tool can be found at

For users that prefer working in an R environment, a wrapper package is provided and can be found and installed from:

PREREQUISITES

The framework is written in PYTHON, however, it also requires the following software with the given versions (or newer):

  • PYTHON version or newer
  • SigProfilerMatrixGenerator (recommended)

QUICK START GUIDE

This section will guide you through the minimum steps required to plot mutational matrices:

  1. Install the python package using pip:
  1. Plot mutational matrices from a Python session or using the Command Line Interface (CLI) as follows:

Using the Python session, the command is as follows:

$ python3>
sigprofiler {sigminer}R Documentation

Extract Signatures with SigProfiler

Description

This function provides an interface to software SigProfiler. More please see Typically, a reference genome is not required because the input is a matrix (my understanding). If you are using refitting result by SigProfiler, please make sure you have input the matrix same order as examples at . If not, use firstly.

Usage

Arguments

a used for NMF decomposition with rows indicate samples and columns indicate components.

output directory.

if , only generate matrix file for SigProfiler so user can call SigProfiler with the input by himself.

signature number range, i.e. .

the number of iteration to be performed to extract each signature number.

if , then refit the denovo signatures with nnls. Same meaning as option in sig_extract or sig_auto_extract.

if , SigProfiler will make denovo to COSMIC sigantures decompostion plots. However, this may fail due to some matrix cannot be identified by SigProfiler plot program.

if , the exomes will be extracted.

the initialization algorithm for W and H matrix of NMF. Options are 'random', 'nndsvd', 'nndsvda'

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