pyscnet.NetEnrich¶
pyscnet.NetEnrich.graph_toolkit¶
Created on Sun Jun 16 20:50:39 2019
@author: mwu
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pyscnet.NetEnrich.graph_toolkit.
buildnet
(gnetdata, key_links, top=None)[source]¶ - Parameters
gnetdata – Gnetdata object.
key_links – str, key of links referring which linkage table for buidling graph
top – int, default None. top ranked links
- Returns
Gnetdata object with graph added into NetAttrs
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pyscnet.NetEnrich.graph_toolkit.
detect_community
(gnetdata, **kwargs)[source]¶ - Parameters
gnetdata – Gnetdata object.
kwargs – additional parameters passed to community_louvain.best_partition()
- Returns
Gnetdata object with ‘communities’ added into NetAttrs
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pyscnet.NetEnrich.graph_toolkit.
find_consensus_graph
(gnetdata, link_key='all', method='intersection', toprank=100, threshold=None, **kwargs)[source]¶ - Parameters
gnetdata – Gnetdata object.
link_key – str, default all. key referring to linkage table.
method – str, default intersection. methods for detecting consensus links. Note: intersection is recommended when there are less than 3 linkage tables.
toprank – int, default 100. top ranked edges for intersection method.
threshold – int, default None. set threshold for ensemble method.
- Returns
Gnetdata object with consensus links added into NetAttrs.
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pyscnet.NetEnrich.graph_toolkit.
get_centrality
(gnetdata)[source]¶ - Parameters
gnetdata – Gnetdata object.
- Returns
gnetData object with ‘centralities’ added into NetAttrs
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pyscnet.NetEnrich.graph_toolkit.
graph_merge
(link_1, link_2, toprank=None, method='union')[source]¶ - Parameters
link_1 – dataframe. linkage table of graph_1
link_2 – dataframe. linkage table of graph_2
toprank – int, default None. top edges from each methods for graph_merge
method – str, default union. methods:[union, intersection, snf]. snf refers to similarity network fusion.
- Returns
dataframe, merged linkage
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pyscnet.NetEnrich.graph_toolkit.
graph_traveral
(graph, start, threshold, method='bfs')[source]¶ - Parameters
graph – network graph object.
start (str) – str. starting point of graph.
threshold – int. the depth-limit
method – str. bfs or dfs
- Returns
explored graph.
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pyscnet.NetEnrich.graph_toolkit.
path_merge
(path_1, path_2, k_mer=3, path='Eulerian')[source]¶ TODO: perform de bruijn graph mapping for ginve two path lists
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pyscnet.NetEnrich.graph_toolkit.
random_walk
(gnetdata, start, supervisedby, steps)[source]¶ - Parameters
gnetdata – Gnetdata object
start – str, starting point of graph.
supervisedby – str, ‘betweenness’, ‘closeness’, ‘degree’ or ‘pageRank’
steps – int, number of steps.
- Returns
a list of travelled nodes.