dotmotif 0.7.0

Find graph motifs using simple, intuitive notation

d o t m o t i f

Find graph motifs using intuitive notation

Usage

Writing a motif

You can currently write motifs in dotmotif form, which is a DSL that specializes in subgraph query notation.

threecycle.motif

# A excites B
A -> B [type = "excitatory"]
# B inhibits C
B -> C [type = "inhibitory"]

Ingesting the motif into dotmotif

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:

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

For more details on how to write a query, see Getting Started.

Citing

If this tool is helpful to your research, please consider citing it with:

# https://www.biorxiv.org/content/10.1101/2020.06.08.140533v1
@article{matelsky_2020_dotmotif,
    doi = {10.1101/2020.06.08.140533},
    url = {https://www.biorxiv.org/content/10.1101/2020.06.08.140533v1},
    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}
}