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Algorithm Arguments
Jordan Matelsky edited this page Mar 18, 2021
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Argument | Type | Default | Description |
---|---|---|---|
motif |
nx.Graph |
The motif to search for. Either a nx.Graph or nx.DiGraph . You can also pass something networkx.Graph -flavored, like a grand.Graph. |
|
host |
nx.Graph |
The "haystack" graph to search within. Either a nx.Graph or nx.DiGraph . You can also pass something networkx.Graph -flavored, like a grand.Graph. |
|
interestingness |
dict |
None |
A lookup dictionary that assigns a floating number between 0 and 1 to each node in the motif graph. Nodes with values closest to 1 will be preferred when the candidate-mapper advances the exploration front. If this doesn't make sense to you, you can ignore this argument entirely. If none is provided, this will default to a uniform interestness metric where all nodes are considered equally. |
count_only |
bool |
False |
Whether to return only a count of motifs, rather than a list of mappings. If you set this to True , you will get back an integer result, not a list of dicts. |
directed |
bool |
None |
Whether to enforce a directed/undirected search. True means enforce directivity; False means enforce undirected search. The default (None) will guess based upon your motif and host. |
profile |
bool |
False |
Whether to slow down execution but give you a better idea of where your RAM usage is going. This is better ignored unless you're debugging something particularly nuanced. |
isomorphisms_only |
bool |
False |
Whether to search only for isomorphisms. In other words, whether to search for edges that exist in the node-induced subgraph. |
hints |
List[Dict[Hashable, Hashable]] |
None |
A list of valid candidate mappings to use as the starting seeds for new maps. See Using Hints, below. |
limit |
int |
None |
An optional integer limit of results to return. If the limit is reached, the search will return early. |
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}
}