HeatCluster SNP Matrix Visualization

Welcome to HeatCluster SNP Matrix Visualization, a Python tool for visualizing SNP (Single Nucleotide Polymorphism) matrices generated via SNP-dists as heatmaps.

Introduction

HeatCluster SNP Matrix Visualization is designed to provide an easy and effective way to visualize SNP matrices. By generating heatmaps from these SNP matrices, it can be easier to identify clusters.

Getting Started

Getting the script

Clone the heatcluster SNP Matrix Visualization repository to your local machine:

git clone https://github.com/DrB-S/heatcluster.git

heatcluster.py can be found in the heatcluster directory which was just created.

Getting the dependencies

heatcluster requires

• python3
  • argparse
  • logging
  • pandas
  • numpy
  • seaborn
  • matplotlib
  • pathlib
  • scipy

pip3 install argparse logging pandas numpy seaborn matplotlib pathlib

Running heatcluster.py

usage: heatcluster.py [-h] -i INPUT [-o OUT] [-t TYPE] [-v]

options:
  -h, --help                show this help message and exit
  -i INPUT, --input INPUT   input SNP matrix file name
  -o OUT, --out OUT         final file name (default = 'SNP_matrix')
  -t TYPE, --type TYPE      file extention for final image (default = 'pdf')
  -v, --version             print version and exit

Multiple test files are located in test which can be used for troubleshooting.

Examples:

heatcluster.py -i test/small_matrix.csv -o small_matrix -t png

This will generate a file called 'small_matrix.png'.

heatcluster.py -i test/large_matrix.csv -o large_matrix

This will generate a file called 'large_matrix.pdf' from a comma-delimited matrix.

Limitations

Currently most outputs from snp-dists are supported with the exception of a molten or melted output (created with the -m option of snp-dists).