Welcome to cagraph’s documentation!

cagraph is a Python library for generating graphs from calcium imaging data of neural activity.

Check out the Usage section for further information, including how to Installation the project.

Note

This project is under active development.

Contents

• Usage
  • Installation
  • Generating CaGraph object
    • CaGraph()
  • Generating graphs
• cagraph
• Installation
• preprocessing
• cagraph
  • CaGraph
    • CaGraph.GraphTheory
      • CaGraph.GraphTheory.compare_graphs()
      • CaGraph.GraphTheory.get_betweenness_centrality()
      • CaGraph.GraphTheory.get_clustering_coefficient()
      • CaGraph.GraphTheory.get_communities()
      • CaGraph.GraphTheory.get_connected_components()
      • CaGraph.GraphTheory.get_correlated_pair_ratio()
      • CaGraph.GraphTheory.get_degree()
      • CaGraph.GraphTheory.get_density()
      • CaGraph.GraphTheory.get_eigenvector_centrality()
      • CaGraph.GraphTheory.get_hubs()
      • CaGraph.GraphTheory.get_largest_connected_component()
      • CaGraph.GraphTheory.get_path_length()
      • CaGraph.GraphTheory.get_smallworld_largest_subnetwork()
      • CaGraph.GraphTheory.graph
      • CaGraph.GraphTheory.neuron_dynamics
      • CaGraph.GraphTheory.node_labels
      • CaGraph.GraphTheory.num_neurons
      • CaGraph.GraphTheory.pearsons_correlation_matrix
      • CaGraph.GraphTheory.time
    • CaGraph.Plotting
      • CaGraph.Plotting.get_single_neuron_timecourse()
      • CaGraph.Plotting.graph
      • CaGraph.Plotting.neuron_dynamics
      • CaGraph.Plotting.num_neurons
      • CaGraph.Plotting.pearsons_correlation_matrix
      • CaGraph.Plotting.plot_all_neurons_timecourse()
      • CaGraph.Plotting.plot_correlation_heatmap()
      • CaGraph.Plotting.plot_multi_neuron_timecourse()
      • CaGraph.Plotting.plot_single_neuron_timecourse()
      • CaGraph.Plotting.time
    • CaGraph.betweenness_centrality
    • CaGraph.clustering_coefficient
    • CaGraph.communities
    • CaGraph.correlated_pair_ratio
    • CaGraph.data
    • CaGraph.dataset_id
    • CaGraph.degree
    • CaGraph.draw_graph()
    • CaGraph.dt
    • CaGraph.get_adjacency_matrix()
    • CaGraph.get_erdos_renyi_graph()
    • CaGraph.get_graph()
    • CaGraph.get_laplacian_matrix()
    • CaGraph.get_pearsons_correlation_matrix()
    • CaGraph.get_random_graph()
    • CaGraph.get_report()
    • CaGraph.get_weight_matrix()
    • CaGraph.graph
    • CaGraph.hubs
    • CaGraph.load()
    • CaGraph.neuron_dynamics
    • CaGraph.node_labels
    • CaGraph.num_neurons
    • CaGraph.pearsons_correlation_matrix
    • CaGraph.reset()
    • CaGraph.save()
    • CaGraph.sensitivity_analysis()
    • CaGraph.threshold
    • CaGraph.time
  • CaGraphBatch
    • CaGraphBatch.dataset_identifiers
    • CaGraphBatch.get_cagraph()
    • CaGraphBatch.get_full_report()
    • CaGraphBatch.group_id
    • CaGraphBatch.load()
    • CaGraphBatch.save()
    • CaGraphBatch.save_individual_dataset_reports()
    • CaGraphBatch.threshold
  • CaGraphBatchTimeSamples
    • CaGraphBatchTimeSamples.dataset_identifiers
    • CaGraphBatchTimeSamples.get_cagraph()
    • CaGraphBatchTimeSamples.get_full_report()
    • CaGraphBatchTimeSamples.group_id
    • CaGraphBatchTimeSamples.load()
    • CaGraphBatchTimeSamples.save()
    • CaGraphBatchTimeSamples.save_individual_dataset_reports()
    • CaGraphBatchTimeSamples.threshold
  • CaGraphBehavior
    • CaGraphBehavior.behavior_identifiers
    • CaGraphBehavior.data
    • CaGraphBehavior.data_id
    • CaGraphBehavior.dt
    • CaGraphBehavior.get_cagraph()
    • CaGraphBehavior.get_full_report()
    • CaGraphBehavior.load()
    • CaGraphBehavior.node_labels
    • CaGraphBehavior.num_neurons
    • CaGraphBehavior.save()
    • CaGraphBehavior.threshold
  • CaGraphMatched
    • CaGraphMatched.data_id
    • CaGraphMatched.dataset_identifiers
    • CaGraphMatched.dt
    • CaGraphMatched.get_cagraph()
    • CaGraphMatched.get_full_report()
    • CaGraphMatched.load()
    • CaGraphMatched.node_labels
    • CaGraphMatched.num_neurons
    • CaGraphMatched.save()
    • CaGraphMatched.threshold
  • CaGraphTimeSamples
    • CaGraphTimeSamples.condition_identifiers
    • CaGraphTimeSamples.data
    • CaGraphTimeSamples.data_id
    • CaGraphTimeSamples.dt
    • CaGraphTimeSamples.get_cagraph()
    • CaGraphTimeSamples.get_full_report()
    • CaGraphTimeSamples.load()
    • CaGraphTimeSamples.node_labels
    • CaGraphTimeSamples.num_neurons
    • CaGraphTimeSamples.save()
    • CaGraphTimeSamples.threshold
• visualization
• Authors
• License

Indices and tables

• Index

• Search Page