How to use the leidenalg.RBERVertexPartition function in leidenalg

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github vtraag / leidenalg / tests / test_VertexPartition.py View on Github external
def setUp(self):
    super(RBERVertexPartitionTest, self).setUp();
    self.partition_type = leidenalg.RBERVertexPartition;
github oscar-franzen / alona / alona / clustering.py View on Github external
log_debug('Running leiden clustering...')
        res = self.params['leiden_res']
        seed = self.params['seed']
        # construct the graph object
        nn = set(self.snn_graph[self.snn_graph.columns[0]])
        g = ig.Graph()
        g.add_vertices(len(nn))
        g.vs['name'] = list(range(1, len(nn)+1))
        ll = []
        for i in self.snn_graph.itertuples(index=False):
            ll.append(tuple(i))
        g.add_edges(ll)
        if self.params == 'ModularityVertexPartition':
            part = leidenalg.ModularityVertexPartition
        else:
            part = leidenalg.RBERVertexPartition
        cl = leidenalg.find_partition(g,
                                      part,
                                      n_iterations=10,
                                      resolution_parameter=res,
                                      seed=seed)
        self.leiden_cl = cl.membership
        self.leiden_prep()
        log_debug('Leiden has finished.')
github logstar / scedar / scedar / cluster / community.py View on Github external
self._sdm = SampleDistanceMatrix(x=x, d=d, metric=metric,
                                         use_pdist=use_pdist,
                                         sids=sids, fids=fids, nprocs=nprocs)
        if graph is None:
            knn_conn_mat = self._sdm.s_knn_connectivity_matrix(
                k=k, use_pca=use_pca, use_hnsw=use_hnsw,
                index_params=index_params, query_params=query_params,
                verbose=verbose)
            graph = SampleDistanceMatrix.knn_conn_mat_to_aff_graph(
                knn_conn_mat, aff_scale=aff_scale)

        if partition_method == "RBConfigurationVertexPartition":
            la_part_cls = la.RBConfigurationVertexPartition
        elif partition_method == "RBERVertexPartition":
            la_part_cls = la.RBERVertexPartition
        elif partition_method == "CPMVertexPartition":
            la_part_cls = la.CPMVertexPartition
        elif partition_method == "SignificanceVertexPartition":
            la_part_cls = la.SignificanceVertexPartition
        elif partition_method == "SurpriseVertexPartition":
            la_part_cls = la.SurpriseVertexPartition
        else:
            raise ValueError(
                "Unknown partition method: {}".format(partition_method))

        la_res = la.find_partition(graph, la.RBConfigurationVertexPartition,
                                   seed=random_state, weights='weight',
                                   resolution_parameter=resolution)
        # keep track of results and parameters
        self._graph = graph
        self._la_res = la_res