HeatMap_Tables
Overview:
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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.
Key Functions:
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.
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Motivation
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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.
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Authorship:
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Author: Rodolfo Aramayo
Work_Email: raramayo@tamu.edu
Personal_Email: rodolfo@aramayo.org
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Copyright:
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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/>.
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Script_Version:
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v1.0.3
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Script_Logic:
-------------------------------------------------------------------------------- See: Code_Overview.md --------------------------------------------------------------------------------
Script_Usage:
-------------------------------------------------------------------------------- See: Mini_Tutorial.md --------------------------------------------------------------------------------
Script_Flags:
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FLAG: "--title"
REQUIRED: Yes
FORMAT: Alphanumeric String
DEFAULT: No default
HELP: Title for the heatmap (use '\\n' for new lines)
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FLAG: "--data"
REQUIRED: Yes
FORMAT: Alphanumeric String
DEFAULT: No default
HELP: Path to the TSV file containing numeric data with headers
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FLAG: "--format"
REQUIRED: No
FORMAT: String
CHOICES: png, pdf
DEFAULT: png
HELP: Output file format (default: png)
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FLAG: "--resolution"
REQUIRED: No
FORMAT: Integer
DEFAULT: 300
HELP: Resolution for PNG output in DPI (default: 300, ignored for PDF)
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FLAG: "--size"
REQUIRED: No
FORMAT: String
CHOICES: small, large
HELP: Override preset font sizes (optional)
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FLAG: "--correction"
REQUIRED: Yes
FORMAT: Float
DEFAULT: 2
HELP: Font color mean correction value (default: 2)
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FLAG: "--palette"
REQUIRED: No
FORMAT: Alphanumeric String
CHOICES: 'Blues', 'viridis', 'coolwarm', 'YlGnBu', 'RdYlGn', 'bwr', 'seismic'
DEFAULT: 'Blues'
HELP: Color scheme for the heatmap.
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FLAG: "--normalize_rows"
REQUIRED: No
FORMAT: Alphanumeric String
ACTION: "Store_True"
CHOICES: "Omitting the flag: == "False""
"Providing the flag: == "True""
HELP: Normalize each row independently (min-max scaling)
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FLAG: "--normalize_columns"
REQUIRED: No
FORMAT: Alphanumeric String
ACTION: "Store_True"
CHOICES: "Omitting the flag: == "False""
"Providing the flag: == "True""
HELP: Normalize each column independently (min-max scaling)
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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
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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)
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FLAG: "-v", "--version"
REQUIRED: No
ACTION: version
FORMAT: Alphanumeric String
HELP: Show program version's number and exit
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FLAG: "-h", "--help"
REQUIRED: No
ACTION: help
FORMAT: Alphanumeric String
HELP: show this help message and exit
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Dependencies:
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Python3: Required:
https://www.python.org/downloads/
Matplotlib: Required:
https://matplotlib.org/
https://pypi.org/project/matplotlib/
Pandas: Required:
https://pandas.pydata.org/docs/index.html
https://pypi.org/project/pandas/
Seaborn: Required:
https://seaborn.pydata.org/
https://pypi.org/project/seaborn/
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Development/Testing Environment:
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Distributor ID: Apple, Inc.
Description: Apple M1 Max
Release: 15.3.1
Codename: 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 |
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Repository:
-------------------------------------------------------------------------------- See: HeatMap_Tables_Python --------------------------------------------------------------------------------
Issues:
-------------------------------------------------------------------------------- See: HeatMap_Tables_Python_Issues --------------------------------------------------------------------------------