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pycomplexheatmap

PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)

https://github.com/dingwb/pycomplexheatmap

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: pubmed.ncbi, ncbi.nlm.nih.gov, wiley.com
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.5%) to scientific vocabulary

Keywords

bioinformatics clustermap complex-heatmaps complexheatmap data-visualization-python heatmap matplotlib pandas plot python single-cell-analysis visualization
Last synced: 6 months ago · JSON representation

Repository

PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)

Basic Info
Statistics
  • Stars: 338
  • Watchers: 5
  • Forks: 35
  • Open Issues: 6
  • Releases: 27
Topics
bioinformatics clustermap complex-heatmaps complexheatmap data-visualization-python heatmap matplotlib pandas plot python single-cell-analysis visualization
Created almost 4 years ago · Last pushed 7 months ago
Metadata Files
Readme Funding License Citation

README.md

PyComplexHeatmap Downloads Downloads Downloads

PyComplexHeatmap is a Python package to plot complex heatmap (clustermap). Please click here for documentation.

Documentation:

https://dingwb.github.io/PyComplexHeatmap

PYPI

Wiki

wiki/layout
wiki/Parameters
wiki/Features

Dependencies:

  • matplotlib<=3.7.5
  • numpy
  • pandas
  • scipy
  • fastcluster pip install --ignore-install matplotlib numpy pandas fastcluster

Citation

Ding, W., Goldberg, D. and Zhou, W. (2023), PyComplexHeatmap: A Python package to visualize multimodal genomics data. iMeta e115. https://doi.org/10.1002/imt2.115
DOI: 10.1002/imt2.115
PMID: 38454967

Installation

  1. Install using pip: ```shell pip install PyComplexHeatmap

upgrade from older version

pip install --upgrade PyComplexHeatmap ```

  1. Install the developmental version directly from github: shell pip install git+https://github.com/DingWB/PyComplexHeatmap # reinstall pip uninstall -y PyComplexHeatmap && pip install git+https://github.com/DingWB/PyComplexHeatmap OR shell git clone https://github.com/DingWB/PyComplexHeatmap cd PyComplexHeatmap python setup.py install

Usage

Simple Guide To Get started

Example output

Click picture to view the source code

Advanced Usage

Kwargs

More Examples

https://dingwb.github.io/PyComplexHeatmap/build/html/more_examples.html

Call for Contributions

The PyComplexHeatmap project welcomes your expertise and enthusiasm!

Small improvements or fixes are always appreciated. If you are considering larger contributions to the source code, please contact us (ding.wu.bin.gm@gmail.com).

Writing code isnt the only way to contribute to PyComplexHeatmap. You can also: - review pull requests - help us stay on top of new and old issues - develop tutorials, presentations, and other educational materials - maintain and improve our website - develop graphic design for our brand assets and promotional materials - translate website content - help with outreach and onboard new contributors - put forward some new ideas about update.

Owner

  • Name: Wubin Ding
  • Login: DingWB
  • Kind: user
  • Location: San Diego
  • Company: Salk Institute for Biological Studies

Working on bioinformatics, computational epigenetics, data visualization, algorithm development, machine learning, and deep learning.

GitHub Events

Total
  • Create event: 4
  • Issues event: 43
  • Release event: 4
  • Watch event: 59
  • Issue comment event: 120
  • Push event: 34
  • Fork event: 5
Last Year
  • Create event: 4
  • Issues event: 43
  • Release event: 4
  • Watch event: 59
  • Issue comment event: 120
  • Push event: 34
  • Fork event: 5

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 143
  • Total Committers: 3
  • Avg Commits per committer: 47.667
  • Development Distribution Score (DDS): 0.014
Top Committers
Name Email Commits
DingWB d****n@1****m 141
Wubin Ding d****m@g****m 1
firefly-cpp i****k@i****u 1
Committer Domains (Top 20 + Academic)
iztok-jr-fister.eu: 1 163.com: 1

Issues and Pull Requests

Last synced: 9 months ago

All Time
  • Total issues: 95
  • Total pull requests: 17
  • Average time to close issues: about 1 month
  • Average time to close pull requests: about 19 hours
  • Total issue authors: 54
  • Total pull request authors: 12
  • Average comments per issue: 4.58
  • Average comments per pull request: 2.0
  • Merged pull requests: 15
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 39
  • Pull requests: 4
  • Average time to close issues: about 1 month
  • Average time to close pull requests: about 14 hours
  • Issue authors: 23
  • Pull request authors: 1
  • Average comments per issue: 4.97
  • Average comments per pull request: 3.0
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • welyt (14)
  • muzier9 (4)
  • faridrashidi (3)
  • Laolga (3)
  • XuejianXiong (3)
  • stephanmg (3)
  • WANGchuang715 (3)
  • z626093820 (3)
  • Xinfeng-Yao (2)
  • GordianArnav (2)
  • verheytb (2)
  • Bo-UT (2)
  • medmaca (1)
  • rtubelleza (1)
  • racng (1)
Pull Request Authors
  • dakomura (4)
  • lingyixu (4)
  • johanneswerner (2)
  • kenibrewer (1)
  • welyt (1)
  • firefly-cpp (1)
  • ajinkya-kulkarni (1)
  • RamRS (1)
  • DingWB (1)
Top Labels
Issue Labels
anno_barplot (2) ticks (1) annotation axis ticks (1)
Pull Request Labels
anno_img (1)

Packages

  • Total packages: 13
  • Total downloads:
    • pypi 1,129 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 85
  • Total maintainers: 2
alpine-v3.18: py3-complexheatmap-pyc

Precompiled Python bytecode for py3-complexheatmap

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 11.2%
Stargazers count: 20.1%
Forks count: 24.5%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 6 months ago
alpine-v3.18: py3-complexheatmap

A Python package to plot complex heatmap (clustermap)

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 11.2%
Stargazers count: 20.1%
Forks count: 24.5%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 6 months ago
pypi.org: pycomplexheatmap

A python package to plot complex heatmap

  • Homepage: https://github.com/DingWB/PyComplexHeatmap
  • Documentation: https://pycomplexheatmap.readthedocs.io/
  • License: MIT License Copyright (c) 2023 Wubin Ding Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  • Latest release: 1.8.2
    published 12 months ago
  • Versions: 53
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 1,129 Last month
Rankings
Dependent packages count: 6.6%
Downloads: 6.8%
Stargazers count: 8.6%
Average: 13.4%
Forks count: 14.5%
Dependent repos count: 30.6%
Maintainers (1)
DingWB
Last synced: 6 months ago
alpine-edge: py3-complexheatmap-pyc

Precompiled Python bytecode for py3-complexheatmap

  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 14.4%
Average: 15.9%
Stargazers count: 22.6%
Forks count: 26.5%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 6 months ago
alpine-edge: py3-complexheatmap

A Python package to plot complex heatmap (clustermap)

  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 14.6%
Average: 16.4%
Stargazers count: 22.9%
Forks count: 28.1%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 6 months ago
alpine-v3.20: py3-complexheatmap-pyc

Precompiled Python bytecode for py3-complexheatmap

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 100%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 6 months ago
alpine-v3.19: py3-complexheatmap

A Python package to plot complex heatmap (clustermap)

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 100%
Last synced: 6 months ago
alpine-v3.19: py3-complexheatmap-pyc

Precompiled Python bytecode for py3-complexheatmap

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 100%
Last synced: 6 months ago
alpine-v3.22: py3-complexheatmap

A Python package to plot complex heatmap (clustermap)

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 100%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 7 months ago
alpine-v3.21: py3-complexheatmap

A Python package to plot complex heatmap (clustermap)

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 100%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 7 months ago
alpine-v3.20: py3-complexheatmap

A Python package to plot complex heatmap (clustermap)

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 100%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 6 months ago
alpine-v3.21: py3-complexheatmap-pyc

Precompiled Python bytecode for py3-complexheatmap

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 100%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 7 months ago
alpine-v3.22: py3-complexheatmap-pyc

Precompiled Python bytecode for py3-complexheatmap

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 100%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 7 months ago

Dependencies

setup.py pypi
  • matplotlib >=3.3.1
  • pandas *
.github/workflows/python-publish.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v3 composite
  • pypa/gh-action-pypi-publish 27b31702a0e7fc50959f5ad993c78deac1bdfc29 composite
pyproject.toml pypi
docs/.eggs/setuptools_scm-8.0.4-py3.8.egg/EGG-INFO/requires.txt pypi
  • build *
  • entangled-cli *
  • mkdocs *
  • mkdocs-entangled-plugin *
  • mkdocs-material *
  • mkdocstrings *
  • packaging >=20
  • pygments *
  • pytest *
  • rich *
  • setuptools *
  • tomli >=1
  • typing-extensions *
  • wheel *