Metadata-Version: 2.1
Name: dotmotif
Version: 0.8.0
Summary: Find graph motifs using simple, intuitive notation
Home-page: https://github.com/aplbrain/dotmotif/tarball/0.8.0
Author: Jordan Matelsky
Author-email: jordan.matelsky@jhuapl.edu
License: ISC
Description: 
        <p align="center">
          <img align="center" src="./logo.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>
        </p>
        
        # Usage
        
        ## Writing a motif
        
        You can currently write motifs in dotmotif form, which is a DSL that specializes in subgraph query notation.
        
        `threecycle.motif`
        
        ```dot
        # A excites B
        A -> B [type = "excitatory"]
        # B inhibits C
        B -> C [type = "inhibitory"]
        ```
        
        ## Ingesting the motif into dotmotif
        
        ```python
        import dotmotif
        
        dm = dotmotif.Motif("threecycle.motif")
        ```
        
        ## Inline code in Python
        
        Alternatively, you can inline your motif in the python code when creating your `dotmotif` object:
        
        ```python
        dm = dotmotif.Motif("""
        # A excites B
        A -> B [type = "excitatory"]
        # B inhibits C
        B -> C [type = "inhibitory"]
        """)
        ```
        
        ## 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://www.biorxiv.org/content/10.1101/2020.06.08.140533v2
        @article{matelsky_2020_dotmotif,
            doi = {10.1101/2020.06.08.140533},
            url = {https://www.biorxiv.org/content/10.1101/2020.06.08.140533v2},
            year = 2020,
            month = {june},
            publisher = {BiorXiv},
            author = {Matelsky, Jordan K. and Reilly, Elizabeth P. and Johnson,Erik C. and Wester, Brock A. and Gray-Roncal, William},
            title = {{Connectome subgraph isomorphisms and graph queries with DotMotif}},
            journal = {BiorXiv}
        }
        ```
        
Keywords: graph,motif
Platform: UNKNOWN
Description-Content-Type: text/markdown
