Genetic Heatmap Tools is a program that creates easy-to-read heatmaps of gene transcription and transcription factor binding data. These heatmaps are a visually attractive method of communicating how transcription factor binding affects gene expression.

Although many Gene Set Enrichment Analysis programs can also be used to create similar heatmaps, those heatmaps are typically cluttered with additional graphs and annotations, rendering them ill-suited for publication:

In contrast, the heatmaps produced by the genetic heatmaps program:

• are completely free of distracting annotations
• use easy-to-read color scales that clearly display the data
• can be expanded to any size without losing resolution

1. Download the installer.

   cd ~/Downloads
   wget https://raw.githubusercontent.com/dennisaldea/genetic-heatmaps/master/installer.sh
   

2. Run the installer.

   ./installer.sh
   

The installer only installs Genetic Heatmap Tools for the user running the script. To install Genetic Heatmap Tools for all users, modify the steps listed in the Manual Installation section.

1. Download the repository.

   cd ~/Downloads
   wget https://github.com/dennisaldea/genetic-heatmaps/archive/master.tar.gz
   

2. Extract the TAR archive.

   tar -xzvf master.tar.gz
   rm master.tar.gz
   

3. Move the extracted files to the ~/.genetic-heatmaps directory.

   mkdir ~/.genetic-heatmaps
   mv -T genetic-heatmaps-master ~/.genetic-heatmaps
   

4. Mark the code files as executable.

   cd ~/.genetic-heatmaps
   chmod 644 *
   chmod 755 src/* INSTALL.sh
   

5. Make a symbolic link to the terminal interface in the ~/bin directory.

   ln -s ~/.genetic-heatmaps/src/terminal-interface.sh ~/bin/ghmtools
   

Genetic Heatmap Tools has three operations, which are described in the table below.

Typical procedure:

1. Input RNA-seq data and either ChIP-seq data or a list of bound genes into the analysis operation.
2. Confirm that the resulting gene activity file was properly created.
3. Input the gene activity file into the heatmap operation.

ghmtools analysis [-f | -i | -n] [-d <binding-distance>] [--no-blacklist] [--window <window-size>] [--] <transcription-data> <binding-data> <genome> <gene-file>

If neither -f, -i, nor -n are given, the -i option is implied.

The analysis operation automatically removes common false positive binding sites from the ChIP-seq data. The ENCODE blacklists are used to identify false positive binding sites. The --no-blacklist option prevents the removal of these blacklisted binding sites.
It is not necessary to specify whether <binding-data> is a ChIP-seq data file or a list of bound genes, since the analysis interface can determine this automatically.

ghmtools analysis foo1.csv foo2.svg mm9 bar.csv

• use the gene transcription data at foo1.csv
• use the gene binding data at foo2.csv
  • create a list of bound genes using the mm9 genome
• create a gene activity file at bar.csv

ghmtools heatmap [-f | -i | -n] [--no-zeros] [--] <gene-data> <transcription-min> <transcription-max> [<binding-max>] <transcription-file> <binding-file>

If neither -f, -i, nor -n are given, the -i option is implied.

If <binding-max> is not given, the maximum value on the gene binding scale is set to the maximum gene binding value in the data.

ghmtools heatmap foo.csv -2.5 2.5 6 bar1.svg bar2.png

• use the data at foo.csv
• create a gene transcription heatmap at bar1.svg
  • scale the transcription scores from -2.5 to 2.5
• create a gene binding heatmap at bar2.png
  • scale the binding scores from 0 to 6

ghmtools help <OPERATION>

If no operation is given, ghmtools help displays a list of operations.

• BASH
  • GNU getopt
• Bedtools
• BETA
• R
  • ggplot2
  • svglite

Copyright 2017 by Dennis Aldea.
Released under the MIT License.