Find graph motifs using intuitive notation
DotMotif is a library that identifies subgraphs or motifs in a large graph. It looks like this:
# Look for all motifs of the form, # Neuron A synapses on Neuron B: A -> B # ...and B inhibits C: B -> C [type = "inhibitory"]| Notebook | Description |
|---|---|
 | Looking for motifs in the IARPA MICrONS Pinky100 Dataset |
| Motif search in a custom graph |
| Subgraph search in the Janelia Hemibrain dataset |
If you have DotMotif, a NetworkX graph, and a curious mind, you already have everything you need to start using DotMotif:
from dotmotif import Motif, GrandIsoExecutor executor = GrandIsoExecutor(graph=my_networkx_graph) triangle = Motif(""" A -> B B -> C C -> A """) results = executor.find(triangle)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.
If this tool is helpful to your research, please consider citing it with:
# 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} }