| Name | PyComplexHeatmap JSON |
| Version |
1.8.0
JSON |
| download |
| home_page | https://github.com/DingWB/PyComplexHeatmap |
| Summary | A python package to plot complex heatmap |
| upload_time | 2024-11-18 05:24:47 |
| maintainer | None |
| docs_url | None |
| author | Wubin Ding |
| requires_python | >=3.0 |
| 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. |
| keywords |
complexheatmap
heatmap
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# PyComplexHeatmap [](https://pepy.tech/project/pycomplexheatmap) [](https://pepy.tech/project/pycomplexheatmap) [](https://pepy.tech/project/pycomplexheatmap)
PyComplexHeatmap is a Python package to plot complex heatmap (clustermap). Please click [here](https://dingwb.github.io/PyComplexHeatmap) for documentation.
## Documentation:
----------------------
[https://dingwb.github.io/PyComplexHeatmap](https://dingwb.github.io/PyComplexHeatmap)
<br><br>
[PYPI](https://pypi.org/project/PyComplexHeatmap/)
<br>
### Wiki
[wiki/layout](../../wiki/Layout/)
<br>
[wiki/Parameters](../../wiki/Parameters/)
<br>
[wiki/Features](../../wiki/Features/)
## Dependencies:
----------------------
- matplotlib>=3.3.1
- 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
<br>
**DOI**: [10.1002/imt2.115](https://onlinelibrary.wiley.com/doi/10.1002/imt2.115)
<br>
**PMID**: [38454967](https://pubmed.ncbi.nlm.nih.gov/38454967/)
## **Installation**
----------------------
1. **Install using pip**:
```shell
pip install PyComplexHeatmap
#upgrade from older version
pip install --upgrade PyComplexHeatmap
```
2. **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**](https://dingwb.github.io/PyComplexHeatmap)
----------------------
### [Simple Guide To Get started](https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/get_started.html)
### Example output
Click picture to view the source code
<table>
<tr style="height: 500px">
<td style="width:33%; background-color:white;text-align:center; vertical-align:middle">
<a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/kwargs.html#Control-gap-&-pad-in-heatmap">
<img src="docs/images/gallery1.png" title="kwargs, gap and pad" align="center" width="250px">
</a>
</td>
<td style="width:33%; background-color:white;text-align:center; vertical-align:middle">
<a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/kwargs.html#Modifying-xlabel-and-ylabel-using-xlabel_kws-and-ylabel_kws">
<img src="docs/images/gallery11.png" title="Modify labels" align="center" width="250px">
</a>
</td>
<td style="width:33%; background-color:white;text-align:center; vertical-align:middle">
<a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/composite_heatmaps.html#Composite-two-heatmaps-horizontally-for-mouse-DNA-methylation-array-dataset">
<img src="docs/images/gallery3.jpg" title="Combine two heatmap horizontally" align="center" width="250px">
</a>
</td>
</tr>
<tr style="height: 500px">
<td style="width:33%; background-color:white;text-align:center; vertical-align:middle">
<a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/advanced_usage.html#Only-plot-the-annotations">
<img src="docs/images/gallery5.png" title="Only plot annotations" align="center" width="250px">
</a>
</td>
<td style="width:33%; background-color:white;text-align:center; vertical-align:middle">
<a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/advanced_usage.html#Cluster-between-groups-and-cluster-within-groups">
<img src="docs/images/gallery6.png" title="Cluster between groups" align="center" width="250px">
</a>
</td>
<td style="width:33%; background-color:white;text-align:center; vertical-align:middle">
<a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/single_cell_methylation.html">
<img src="docs/images/gallery9.png" title="DNA methylation cell type specific signatures" align="center" width="250px">
</a>
</td>
</tr>
<tr style="height: 500px">
<td style="width:33%; background-color:white;text-align:center; vertical-align:middle">
<a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/oncoPrint.html">
<img src="docs/images/gallery8.png" title="OncoPrint with columns split" align="center" width="250px">
</a>
</td>
<td style="width:33%; background-color:white;text-align:center; vertical-align:middle">
<a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/dotHeatmap.html#Visualize-up-to-five-dimension-data-using-DotClustermapPlotter">
<img src="docs/images/gallery7.png" title="Dot clustermap to show enrichment result" align="center" width="250px">
</a>
</td>
<td style="width:33%; background-color:white;text-align:center; vertical-align:middle">
<a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/oncoPrint2.html">
<img src="docs/images/gallery4.png" title="Visualizing categorical variables using oncoPrint" align="center" width="250px">
</a>
</td>
</tr>
<tr style="height: 500px">
<td style="width:33%; background-color:white;text-align:center; vertical-align:middle">
<a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/cpg_modules.html#Plotting-the-Dot-clustermap">
<img src="docs/images/gallery2.png" title="Dot clustermap with annotations" align="center" width="250px">
</a>
</td>
<td style="width:33%; background-color:white;text-align:center; vertical-align:middle">
<a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/advanced_usage.html#Custom-annotation">
<img src="docs/images/gallery10.png" title="Custom annotation" align="center" width="250px">
</a>
</td>
<td style="width:33%; background-color:white;text-align:center; vertical-align:middle">
<a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/gene_enrichment_analysis.html#Plot">
<img src="docs/images/gallery12.png" title="Plot only the annotation with different orientations" align="center" width="250px">
</a>
</td>
</tr>
</table>
### [Advanced Usage](https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/advanced_usage.html)
### [Kwargs](https://dingwb.github.io/PyComplexHeatmap/build/html/kwargs.html)
## **More Examples**
[https://dingwb.github.io/PyComplexHeatmap/build/html/more_examples.html](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 isn’t 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](https://dingwb.github.io/PyComplexHeatmap)
- 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.
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"description": "# PyComplexHeatmap [](https://pepy.tech/project/pycomplexheatmap) [](https://pepy.tech/project/pycomplexheatmap) [](https://pepy.tech/project/pycomplexheatmap)\nPyComplexHeatmap is a Python package to plot complex heatmap (clustermap). Please click [here](https://dingwb.github.io/PyComplexHeatmap) for documentation.\n\n## Documentation:\n----------------------\n[https://dingwb.github.io/PyComplexHeatmap](https://dingwb.github.io/PyComplexHeatmap)\n<br><br>\n[PYPI](https://pypi.org/project/PyComplexHeatmap/)\n<br>\n\n### Wiki\n[wiki/layout](../../wiki/Layout/)\n<br>\n[wiki/Parameters](../../wiki/Parameters/)\n<br>\n[wiki/Features](../../wiki/Features/)\n\n## Dependencies:\n----------------------\n- matplotlib>=3.3.1\n- numpy\n- pandas\n- scipy\n- fastcluster\n```\npip install --ignore-install matplotlib numpy pandas fastcluster\n```\n\n## Citation\nDing, 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\n<br>\n**DOI**: [10.1002/imt2.115](https://onlinelibrary.wiley.com/doi/10.1002/imt2.115)\n<br>\n**PMID**: [38454967](https://pubmed.ncbi.nlm.nih.gov/38454967/)\n\n## **Installation**\n----------------------\n1. **Install using pip**:\n```shell\npip install PyComplexHeatmap\n\n#upgrade from older version\npip install --upgrade PyComplexHeatmap\n```\n\n2. **Install the developmental version directly from github**:\n```shell\npip install git+https://github.com/DingWB/PyComplexHeatmap\n# reinstall\npip uninstall -y PyComplexHeatmap && pip install git+https://github.com/DingWB/PyComplexHeatmap\n```\nOR\n```shell\ngit clone https://github.com/DingWB/PyComplexHeatmap\ncd PyComplexHeatmap\npython setup.py install\n```\n\n## [**Usage**](https://dingwb.github.io/PyComplexHeatmap)\n----------------------\n### [Simple Guide To Get started](https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/get_started.html)\n### Example output\nClick picture to view the source code\n\n<table>\n <tr style=\"height: 500px\">\n <td style=\"width:33%; background-color:white;text-align:center; vertical-align:middle\">\n <a href=\"https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/kwargs.html#Control-gap-&-pad-in-heatmap\">\n <img src=\"docs/images/gallery1.png\" title=\"kwargs, gap and pad\" align=\"center\" width=\"250px\">\n </a>\n </td>\n <td style=\"width:33%; background-color:white;text-align:center; vertical-align:middle\">\n <a href=\"https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/kwargs.html#Modifying-xlabel-and-ylabel-using-xlabel_kws-and-ylabel_kws\">\n <img src=\"docs/images/gallery11.png\" title=\"Modify labels\" align=\"center\" width=\"250px\">\n </a>\n </td>\n <td style=\"width:33%; background-color:white;text-align:center; vertical-align:middle\">\n <a href=\"https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/composite_heatmaps.html#Composite-two-heatmaps-horizontally-for-mouse-DNA-methylation-array-dataset\">\n <img src=\"docs/images/gallery3.jpg\" title=\"Combine two heatmap horizontally\" align=\"center\" width=\"250px\">\n </a>\n </td>\n </tr>\n <tr style=\"height: 500px\">\n <td style=\"width:33%; background-color:white;text-align:center; vertical-align:middle\">\n <a href=\"https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/advanced_usage.html#Only-plot-the-annotations\">\n <img src=\"docs/images/gallery5.png\" title=\"Only plot annotations\" align=\"center\" width=\"250px\">\n </a>\n </td>\n <td style=\"width:33%; background-color:white;text-align:center; vertical-align:middle\">\n <a href=\"https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/advanced_usage.html#Cluster-between-groups-and-cluster-within-groups\">\n <img src=\"docs/images/gallery6.png\" title=\"Cluster between groups\" align=\"center\" width=\"250px\">\n </a>\n </td>\n <td style=\"width:33%; background-color:white;text-align:center; vertical-align:middle\">\n <a href=\"https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/single_cell_methylation.html\">\n <img src=\"docs/images/gallery9.png\" title=\"DNA methylation cell type specific signatures\" align=\"center\" width=\"250px\">\n </a>\n </td>\n </tr>\n <tr style=\"height: 500px\">\n <td style=\"width:33%; background-color:white;text-align:center; vertical-align:middle\">\n <a href=\"https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/oncoPrint.html\">\n <img src=\"docs/images/gallery8.png\" title=\"OncoPrint with columns split\" align=\"center\" width=\"250px\">\n </a>\n </td>\n <td style=\"width:33%; background-color:white;text-align:center; vertical-align:middle\">\n <a href=\"https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/dotHeatmap.html#Visualize-up-to-five-dimension-data-using-DotClustermapPlotter\">\n <img src=\"docs/images/gallery7.png\" title=\"Dot clustermap to show enrichment result\" align=\"center\" width=\"250px\">\n </a>\n </td>\n <td style=\"width:33%; background-color:white;text-align:center; vertical-align:middle\">\n <a href=\"https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/oncoPrint2.html\">\n <img src=\"docs/images/gallery4.png\" title=\"Visualizing categorical variables using oncoPrint\" align=\"center\" width=\"250px\">\n </a>\n </td>\n </tr>\n <tr style=\"height: 500px\">\n <td style=\"width:33%; background-color:white;text-align:center; vertical-align:middle\">\n <a href=\"https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/cpg_modules.html#Plotting-the-Dot-clustermap\">\n <img src=\"docs/images/gallery2.png\" title=\"Dot clustermap with annotations\" align=\"center\" width=\"250px\">\n </a>\n </td>\n <td style=\"width:33%; background-color:white;text-align:center; vertical-align:middle\">\n <a href=\"https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/advanced_usage.html#Custom-annotation\">\n <img src=\"docs/images/gallery10.png\" title=\"Custom annotation\" align=\"center\" width=\"250px\">\n </a>\n </td>\n <td style=\"width:33%; background-color:white;text-align:center; vertical-align:middle\">\n <a href=\"https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/gene_enrichment_analysis.html#Plot\">\n <img src=\"docs/images/gallery12.png\" title=\"Plot only the annotation with different orientations\" align=\"center\" width=\"250px\">\n </a>\n </td>\n </tr>\n</table>\n\n### [Advanced Usage](https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/advanced_usage.html)\n\n### [Kwargs](https://dingwb.github.io/PyComplexHeatmap/build/html/kwargs.html)\n\n## **More Examples**\n[https://dingwb.github.io/PyComplexHeatmap/build/html/more_examples.html](https://dingwb.github.io/PyComplexHeatmap/build/html/more_examples.html)\n\n## Call for Contributions\n----------------------\n\nThe PyComplexHeatmap project welcomes your expertise and enthusiasm!\n\nSmall improvements or fixes are always appreciated. If you are considering larger contributions\nto the source code, please contact us (ding.wu.bin.gm@gmail.com).\n\nWriting code isn\u2019t the only way to contribute to PyComplexHeatmap. You can also:\n- review pull requests\n- help us stay on top of new and old issues\n- develop tutorials, presentations, and other educational materials\n- maintain and improve [our website](https://dingwb.github.io/PyComplexHeatmap)\n- develop graphic design for our brand assets and promotional materials\n- translate website content\n- help with outreach and onboard new contributors\n- put forward some new ideas about update.\n",
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