The script reads a TSV file containing numeric data and generates a heatmap visualization.
It is designed to be flexible by adjusting fonts and figure size based on the input data dimensions.
- Argument Parsing:
Uses Python’s argparse to capture the title, data file, output format, resolution, optional size settings, and a correction factor for text color thresholds.
- Data Loading and Preprocessing:
Reads the TSV file with Pandas, filters out unwanted rows (e.g., those with "TOTAL:"), converts specific percentage values if necessary, and ensures all selected columns are numeric.
- Dynamic Visualization Settings:
Auto-detects if the data is "large" (more than 50 rows or 6 columns) and adjusts font sizes and figure dimensions accordingly.
- Heatmap Generation:
Uses Seaborn to create the heatmap. Data values are annotated in each cell, and text colors are dynamically adjusted based on how the cell’s value compares to the overall mean (modified by a correction factor).
- Output:
Saves the generated heatmap as a PNG (with a configurable DPI) or as a PDF.
The script was developed to display numerical values in a table format while using color to visually emphasize the magnitude and variations of those values.
- Author: Rodolfo Aramayo
- Work_Email: raramayo@tamu.edu
- Personal_Email: rodolfo@aramayo.org
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.
- v1.0.4
Code_Overview.md
Mini_Tutorial.md
--------------------------------------------------------------------------------
FLAG: "--title"
REQUIRED: Yes
FORMAT: Alphanumeric String = '--title'
DEFAULT: No default
HELP: Title for the heatmap (use '\\n' for new lines)
----------------------------------------------------------------
FLAG: "--data"
REQUIRED: Yes
FORMAT: Alphanumeric String = '--data'
DEFAULT: No default
HELP: Path to the TSV file containing numeric data with headers
----------------------------------------------------------------
FLAG: "--format"
REQUIRED: No
FORMAT: String
CHOICES: 'png', 'pdf'
DEFAULT: 'png'
HELP: Output file format
----------------------------------------------------------------
FLAG: "--resolution"
REQUIRED: No
FORMAT: Integer
DEFAULT: '300'
HELP: Resolution for 'png' output in 'DPI'
Ignored for 'pdf'
--------------------------------------------------------------------------------
FLAG: "--size"
REQUIRED: No
FORMAT: String
CHOICES: 'small', 'large'
DEFAULT: No default
HELP: Override preset font sizes (optional)
---------------------------------------------------------------
FLAG: "--correction"
REQUIRED: Yes
FORMAT: Float
DEFAULT: '2'
HELP: Font color mean correction value
---------------------------------------------------------------
FLAG: "--palette"
REQUIRED: No
FORMAT: Alphanumeric String
CHOICES: 'Blues', 'viridis', 'coolwarm', 'YlGnBu', 'RdYlGn', 'bwr', 'seismic'
DEFAULT: 'Blues'
HELP: Color scheme for the heatmap
---------------------------------------------------------------
FLAG: "--normalize_rows"
REQUIRED: No
FORMAT: Alphanumeric String = '--normalize_rows'
CHOICES: Omitting the flag: == 'False'
Providing the flag: == 'True'
ACTION: store_true
DEFAULT: 'False'
HELP: Normalize each row independently (min-max scaling)
---------------------------------------------------------------
FLAG: "--normalize_columns"
REQUIRED: No
FORMAT: Alphanumeric String = '--normalize_columns'
CHOICES: Omitting the flag: == 'False'
Providing the flag: == 'True'
ACTION: store_true
DEFAULT: 'False'
HELP: Normalize each column independently (min-max scaling)
---------------------------------------------------------------
FLAG: "--cell_font_size"
REQUIRED: No
FORMAT: Integer
DEFAULT: '12'
HELP: Override cell annotation font size (e.g., 20)
Font Size Default for Large Tables: 8
Font Size Default for Small Tables: 12
---------------------------------------------------------------
FLAG: "cell_height"
REQUIRED: No
FORMAT: Integer
DEFAULT: '1.5'
HELP: Set the height (in inches) for each cell
Figure height is computed as (number of rows) x (cell height)
---------------------------------------------------------------
FLAG: "-v", "--version"
REQUIRED: No
ACTION: version
FORMAT: Alphanumeric String
HELP: Show program version's number and exit
--------------------------------------------------------------------------------
FLAG: "-h", "--help"
REQUIRED: No
ACTION: help
FORMAT: Alphanumeric String
HELP: show this help message and exit
--------------------------------------------------------------------------------
| Distributor ID | Description | Release | Codename |
|---|---|---|---|
| Apple, Inc. | Apple M1 Max | 15.3.1 | Sequoia |
- Script was tested with:
| Python Version | matplotlib | pandas | seaborn |
|---|---|---|---|
| 3.8.20 | 3.7.5 | 2.0.3 | 0.13.2 |
| 3.9.21 | 3.9.4 | 2.2.3 | 0.13.2 |
| 3.10.16 | 3.10.1 | 2.2.3 | 0.13.2 |
| 3.11.11 | 3.10.1 | 2.2.3 | 0.13.2 |
| 3.12.9 | 3.10.1 | 2.2.3 | 0.13.2 |
| 3.13.2 | 3.10.1 | 2.2.3 | 0.13.2 |
HeatMap_Tables_Python
HeatMap_Tables_Python_Issues
@misc{RN165,
author = {Aramayo, Rodolfo},
title = {HeatMap_Tables_Python},
publisher = {CERN Data Centre & InvenioRDM},
month = {2025-04-14},
keywords = {Bioinformatics
comparative genomics
ensembl
gene annotation
genome annotation
genome browsers},
DOI = {10.5281/zenodo.15214452},
url = {https://doi.org/10.5281/zenodo.15214452},
year = {2025},
type = {Dataset}
}