Circular Layout: Chemical Evolution Reactions
Description
Dataset Description: Circular Layout of Chemical Evolution Reactions Overview This dataset represents a directed graph that visualizes the relationships between various chemical reactions involved in chemical evolution. The graph is constructed using the NetworkX library and illustrates the connections between reactants and products, with edge weights indicating the frequency or significance of each reaction. The visualization employs a circular layout to enhance clarity and facilitate understanding of the interactions. Data Structure The graph consists of nodes and directed edges: Nodes: Represent the chemical compounds or processes involved in the reactions, such as "Formaldehyde," "Strecker Synthesis," "Amino Acids," and "Fatty Acids." Edges: Directed edges connect nodes, indicating the flow from reactants to products. Each edge is associated with a weight that quantifies the frequency of the reaction. Visualization The graph is visualized using a circular layout, which organizes nodes in a circular pattern for easy interpretation of relationships. The following features enhance the visualization: Node Color: All nodes are colored light blue for uniformity. Edge Color: Edges are colored based on their weights, using a plasma colormap to represent frequency visually. Darker colors indicate higher weights, while lighter colors correspond to lower weights. Arrowheads: Directed arrows indicate the flow of reactions from reactants to products. Color Bar A color bar is included to provide context for edge weights: Label: "Reaction Weight (Frequency)" indicates what the colors represent. Scale: The color bar ranges from the minimum to maximum weight values, allowing viewers to gauge the significance of each reaction based on edge color. Title and Styling The title of the visualization is "Circular Layout: Chemical Evolution Reactions," reflecting its focus on illustrating key reactions in chemical evolution. The axes are turned off to emphasize the relationships without distraction. Conclusion This dataset provides a comprehensive visual representation of chemical evolution reactions, highlighting key pathways and their frequencies. By analyzing this graph, researchers can gain insights into which reactions play a more prominent role in chemical evolution processes, facilitating further exploration into the origins of life on Earth.
Files
Steps to reproduce
import networkx as nx import matplotlib.pyplot as plt # Define edges with weights edges_with_weights = [ ("Formaldehyde", "Strecker Synthesis", 80), ("Hydrogen Cyanide", "Strecker Synthesis", 90), ("Strecker Synthesis", "Amino Acids", 100), ("Hydrogen Cyanide", "Purines", 70), ("UV Radiation", "Purines", 65), ("Hydrogen Cyanide", "Pyrimidines", 60), ("UV Radiation", "Pyrimidines", 55), ("Formaldehyde", "Formose Reaction", 85), ("Minerals", "Formose Reaction", 75), ("Formose Reaction", "Ribose", 95), ("Fischer-Tropsch Synthesis", "Fatty Acids", 90), ("Fatty Acids", "Micelles", 88), ("Fatty Acids", "Bilayers", 92), ] # Create a directed graph G = nx.DiGraph() # Add edges with weights for u, v, w in edges_with_weights: G.add_edge(u, v, weight=w) # Extract edge weights weights = [G[u][v]['weight'] for u, v in G.edges] # Circular layout pos = nx.circular_layout(G) # Draw the graph plt.figure(figsize=(12, 10)) nodes = nx.draw_networkx_nodes(G, pos, node_size=3000, node_color='lightblue') edges = nx.draw_networkx_edges(G, pos, arrowstyle='->', arrowsize=15, edge_color=weights, edge_cmap=plt.cm.plasma, edge_vmin=min(weights), edge_vmax=max(weights)) labels = nx.draw_networkx_labels(G, pos, font_size=10, font_weight='bold') # Add a color bar for edge weights sm = plt.cm.ScalarMappable(cmap=plt.cm.plasma, norm=plt.Normalize(vmin=min(weights), vmax=max(weights))) sm.set_array([]) cbar = plt.colorbar(sm) cbar.set_label('Reaction Weight (Frequency)', fontsize=12) # Title and styling plt.title("Circular Layout: Chemical Evolution Reactions", fontsize=14) plt.axis('off') # Turn off axes plt.show()