Source code for graphein.rna.visualisation

"""Visualisation utilities for RNA Secondary Structure Graphs."""
# %%
# Graphein
# Author: Arian Jamasb <>
# License: MIT
# Project Website:
# Code Repository:

import logging
from collections import defaultdict
from itertools import chain
from typing import Dict, List

import networkx as nx

from graphein.rna.graphs import RNA_BASE_COLORS

log = logging.getLogger(__name__)

[docs]def plot_rna_graph( g: nx.Graph, layout: nx.layout = nx.layout.circular_layout, label_base_type: bool = True, label_base_position: bool = False, label_dotbracket_symbol: bool = False, **kwargs, ): """Plots a RNA Secondary Structure Graph. Colours edges by kind. :param g: NetworkX graph of RNA secondary structure graph. :type g: nx.Graph :param layout: Layout algorithm to use. Default is circular_layout. :type layout: nx.layout :param label_base_type: Whether to label the base type of each base. :type label_base_type: bool :param label_base_position: Whether to label the base position of each base. :type label_base_position: bool :param label_dotbracket_symbol: Whether to label the dotbracket symbol of each base. """ edge_colors = nx.get_edge_attributes(g, "color").values() node_colors = nx.get_node_attributes(g, "color").values() if len(node_colors) == 0: node_colors = None if len(edge_colors) == 0: edge_colors = None # Construct node labelling scheme node_label_dicts: List[Dict[int, str]] = [] if label_base_type: try: node_label_dicts.append( {n: d["nucleotide"] for n, d in g.nodes(data=True)} ) except KeyError: log.warning( "No sequence data found in graph. Skipping base type labelling." ) if label_base_position: node_label_dicts.append({n: str(n) for n in g.nodes()}) elif label_dotbracket_symbol: node_label_dicts.append( {n: d["dotbracket_symbol"] for n, d in g.nodes(data=True)} ) node_labels = defaultdict(str) for key, value in chain.from_iterable(map(dict.items, node_label_dicts)): node_labels[key] += value nx.draw( g, node_color=node_colors, edge_color=edge_colors, with_labels=True, labels=node_labels, pos=layout(g), **kwargs, )