Set up the network.

         Filter genes out if requested and add attributes to the vertices.

        :param genes: A list of Gene objects.
        :param gene_filter: Removes all genes that are not in list <genes> if True.
        :param disease_associations: Diseases associated with genes.

def set_up_network(
            self,
            genes: List[Gene],
            gene_filter: bool = False,
            disease_associations: Optional[Dict] = None
    ) -> None:
        """Set up the network.

         Filter genes out if requested and add attributes to the vertices.

        :param genes: A list of Gene objects.
        :param gene_filter: Removes all genes that are not in list <genes> if True.
        :param disease_associations: Diseases associated with genes.
        """
        if gene_filter:
            self.filter_genes([gene.entrez_id for gene in genes])
        self._add_vertex_attributes(genes, disease_associations)
        self.print_summary("Graph of all genes")