<p align="center">
<img align="center" src="https://user-images.githubusercontent.com/693511/117350563-b58b9900-ae7a-11eb-83ce-9f5f9213145e.png" / width="25%">
<h1 align="center" fontsize="2em">d o t m o t i f</h1>
</p>
<p align="center">Find graph motifs using intuitive notation</p>
<p align="center">
<a href="https://pypi.org/project/dotmotif/"><img alt="PyPI" src="https://img.shields.io/pypi/v/dotmotif?style=for-the-badge"></a>
<a href="https://bossdb.org/tools/DotMotif"><img src="https://img.shields.io/badge/Pretty Dope-👌-00ddcc.svg?style=for-the-badge" /></a>
<a href="https://bossdb.org/tools/DotMotif"><img src="https://img.shields.io/badge/License-Apache_2.0-blue.svg?style=for-the-badge" /></a>
<a href="https://codecov.io/gh/aplbrain/dotmotif"><img alt="Codecov" src="https://img.shields.io/codecov/c/github/aplbrain/dotmotif?style=for-the-badge"></a>
</p>
---
DotMotif is a library that identifies subgraphs or motifs in a large graph. It looks like this:
```py
# Look for all motifs of the form,
# Neuron A synapses on Neuron B:
A -> B
# ...and B inhibits C:
B -> C [type = "inhibitory"]
```
# Examples
| Notebook | Description |
|----------|-------------|
| <a href="https://colab.research.google.com/gist/j6k4m8/7c5cf55e7feb24685bd13a217cedda1d/dotmotif-search-in-pinky100.ipynb" target="_parent"><img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/></a> | Looking for motifs in the IARPA MICrONS Pinky100 Dataset |
| <a href="https://colab.research.google.com/gist/j6k4m8/d02259dfedc2321973be4d2e665653f4/dotmotif-search-in-custom-networkx.ipynb" target="_parent"><img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/></a> | Motif search in a custom graph |
| <a href="https://colab.research.google.com/gist/j6k4m8/919cc1a8162289dd4a6aeb965e800322/dotmotif-search-in-custom-networkx.ipynb" target="_parent"><img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/></a> | Subgraph search in the Janelia Hemibrain dataset |
# Get Started
If you have [DotMotif](https://github.com/aplbrain/dotmotif/wiki/Installation), a NetworkX graph, and a curious mind, you already have everything you need to start using DotMotif:
```python
from dotmotif import Motif, GrandIsoExecutor
executor = GrandIsoExecutor(graph=my_networkx_graph)
triangle = Motif("""
A -> B
B -> C
C -> A
""")
results = executor.find(triangle)
```
# Parameters
You can also pass optional parameters into the constructor for the `dotmotif` object. Those arguments are:
| Argument | Type, Default | Behavior |
| ----------------------- | --------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| `ignore_direction` | `bool`: `False` | Whether to disregard direction when generating the database query |
| `limit` | `int`: `None` | A limit (if any) to impose on the query results |
| `enforce_inequality` | `bool`: `False` | Whether to enforce inequality; in other words, whether two nodes should be permitted to be aliases for the same node. For example, in `A->B->C`; if `A!=C`, then set to `True` |
| `exclude_automorphisms` | `bool`: `False` | Whether to return only a single example for each detected automorphism. See more in [the documentation](https://github.com/aplbrain/dotmotif/wiki/Automorphisms) |
For more details on how to write a query, see [Getting Started](https://github.com/aplbrain/dotmotif/wiki/Getting-Started).
---
# Citing
If this tool is helpful to your research, please consider citing it with:
```bibtex
# https://doi.org/10.1038/s41598-021-91025-5
@article{Matelsky_Motifs_2021,
title={{DotMotif: an open-source tool for connectome subgraph isomorphism search and graph queries}},
volume={11},
ISSN={2045-2322},
url={http://dx.doi.org/10.1038/s41598-021-91025-5},
DOI={10.1038/s41598-021-91025-5},
number={1},
journal={Scientific Reports},
publisher={Springer Science and Business Media LLC},
author={Matelsky, Jordan K. and Reilly, Elizabeth P. and Johnson, Erik C. and Stiso, Jennifer and Bassett, Danielle S. and Wester, Brock A. and Gray-Roncal, William},
year={2021},
month={Jun}
}
```
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"description": "<p align=\"center\">\n <img align=\"center\" src=\"https://user-images.githubusercontent.com/693511/117350563-b58b9900-ae7a-11eb-83ce-9f5f9213145e.png\" / width=\"25%\">\n <h1 align=\"center\" fontsize=\"2em\">d o t m o t i f</h1>\n</p>\n<p align=\"center\">Find graph motifs using intuitive notation</p>\n\n<p align=\"center\">\n<a href=\"https://pypi.org/project/dotmotif/\"><img alt=\"PyPI\" src=\"https://img.shields.io/pypi/v/dotmotif?style=for-the-badge\"></a>\n<a href=\"https://bossdb.org/tools/DotMotif\"><img src=\"https://img.shields.io/badge/Pretty Dope-\ud83d\udc4c-00ddcc.svg?style=for-the-badge\" /></a>\n<a href=\"https://bossdb.org/tools/DotMotif\"><img src=\"https://img.shields.io/badge/License-Apache_2.0-blue.svg?style=for-the-badge\" /></a>\n<a href=\"https://codecov.io/gh/aplbrain/dotmotif\"><img alt=\"Codecov\" src=\"https://img.shields.io/codecov/c/github/aplbrain/dotmotif?style=for-the-badge\"></a>\n</p>\n\n---\n\nDotMotif is a library that identifies subgraphs or motifs in a large graph. It looks like this:\n\n```py\n# Look for all motifs of the form,\n\n# Neuron A synapses on Neuron B:\nA -> B\n# ...and B inhibits C:\nB -> C [type = \"inhibitory\"]\n```\n\n# Examples\n\n| Notebook | Description |\n|----------|-------------|\n| <a href=\"https://colab.research.google.com/gist/j6k4m8/7c5cf55e7feb24685bd13a217cedda1d/dotmotif-search-in-pinky100.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a> | Looking for motifs in the IARPA MICrONS Pinky100 Dataset |\n| <a href=\"https://colab.research.google.com/gist/j6k4m8/d02259dfedc2321973be4d2e665653f4/dotmotif-search-in-custom-networkx.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a> | Motif search in a custom graph |\n| <a href=\"https://colab.research.google.com/gist/j6k4m8/919cc1a8162289dd4a6aeb965e800322/dotmotif-search-in-custom-networkx.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a> | Subgraph search in the Janelia Hemibrain dataset |\n\n\n# Get Started\n\nIf you have [DotMotif](https://github.com/aplbrain/dotmotif/wiki/Installation), a NetworkX graph, and a curious mind, you already have everything you need to start using DotMotif:\n\n```python\nfrom dotmotif import Motif, GrandIsoExecutor\n\nexecutor = GrandIsoExecutor(graph=my_networkx_graph)\n\ntriangle = Motif(\"\"\"\nA -> B\nB -> C\nC -> A\n\"\"\")\n\nresults = executor.find(triangle)\n```\n\n# Parameters\n\nYou can also pass optional parameters into the constructor for the `dotmotif` object. Those arguments are:\n\n| Argument | Type, Default | Behavior |\n| ----------------------- | --------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |\n| `ignore_direction` | `bool`: `False` | Whether to disregard direction when generating the database query |\n| `limit` | `int`: `None` | A limit (if any) to impose on the query results |\n| `enforce_inequality` | `bool`: `False` | Whether to enforce inequality; in other words, whether two nodes should be permitted to be aliases for the same node. For example, in `A->B->C`; if `A!=C`, then set to `True` |\n| `exclude_automorphisms` | `bool`: `False` | Whether to return only a single example for each detected automorphism. See more in [the documentation](https://github.com/aplbrain/dotmotif/wiki/Automorphisms) |\n\nFor more details on how to write a query, see [Getting Started](https://github.com/aplbrain/dotmotif/wiki/Getting-Started).\n\n---\n\n# Citing\n\nIf this tool is helpful to your research, please consider citing it with:\n\n```bibtex\n# https://doi.org/10.1038/s41598-021-91025-5\n@article{Matelsky_Motifs_2021, \n title={{DotMotif: an open-source tool for connectome subgraph isomorphism search and graph queries}},\n volume={11}, \n ISSN={2045-2322}, \n url={http://dx.doi.org/10.1038/s41598-021-91025-5}, \n DOI={10.1038/s41598-021-91025-5}, \n number={1}, \n journal={Scientific Reports}, \n publisher={Springer Science and Business Media LLC}, \n author={Matelsky, Jordan K. and Reilly, Elizabeth P. and Johnson, Erik C. and Stiso, Jennifer and Bassett, Danielle S. and Wester, Brock A. and Gray-Roncal, William},\n year={2021}, \n month={Jun}\n}\n```\n",
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