Package index • ggNetView

Network builders

Construct a tidygraph network object from various input types. All builders return a module-annotated graph ready for ggNetView().

build_graph_from_mat(): Build a correlation-based network from a matrix
build_graph_from_double_mat(): Build a graph object from Two numeric matrix
build_graph_from_double_mat_with_module(): Build a graph object from Two numeric matrix
build_graph_from_multi_mat(): Build a graph object from multiple numeric matrices
build_graph_from_adj_mat(): Build a correlation-based network from a adjacency matrix
build_graph_from_adj_mat_module(): Build a graph object from a adjacency matrix and module Info
build_graph_from_df(): Build a graph object from a data frame
build_graph_from_igraph(): Build a graph object from a graph object
build_graph_from_module(): Build a graph object from a data frame and module Info
build_graph_from_wgcna(): Build a graph object from WGCNA result
build_graph_from_pie(): Build a pie graph object from a data frame
build_graph_from_enrichGO(): Build a graph object from GO enrichment analysis
build_graph_from_consensus(): Build a consensus graph object from multiple adjacency matrices
build_graph_from_node_edge(): Build a graph object from separate node and edge tables
build_graph_from_stringdb(): Build a graph object from a STRING database export

Plot networks, heatmaps, and multi-network comparisons.

ggNetView(): Visualize a network with custom layouts
ggNetView_multi(): Visualize network with custom layouts in different samples
ggNetView_multi_link(): Visualize multiple networks and show the connections between them to highlight key members within the networks
gglink_heatmaps(): Multi-orientation species-environment correlation / Mantel heatmap
gglink_heatmaps_2(): Visualize multi-orientation environmental-species correlation heatmaps (adaptive sizing)
gglink_heatmap_triple(): Visualize multi-orientation environmental-species correlation heatmaps2
ggnetview_modularity_heatmaps(): Network + module-environment heatmaps with shared Mantel API
ggnetview_subgraph(): Visualize a network with a magnified (zoomed) module subgraph
ggnetview_zipi(): Compute Zi-Pi (within-module connectivity and participation coefficient)
ggnetview_perturbation_curve(): Plot a network perturbation (attack) curve

Compute topology metrics, extract subgraphs, and perform statistical tests.

get_network_topology(): Create network topology
get_network_topology_parallel(): Create network topology in parallel
get_sample_subgraph(): Extract sample-level subgraphs from a graph object
get_sample_subgraph_topology(): Create sample-level subgraph topology from a global network
get_sample_subgraph_topology_parallel(): Create sample-level subgraph topology in parallel
get_network_perturbation(): Structural perturbation ("virtual attack") of a network
get_node_influence(): Propagate a virtual perturbation from source node(s) across the network
get_node_centrality(): Compute per-node centralities and attach them to a graph object
get_node_ivi(): Compute the Integrated Value of Influence (IVI) per node
press_perturbation(): Press-perturbation (sustained-disturbance) analysis
ggNetView_RMT(): One-shot, non-interactive RMT threshold scan with auto selection
mantel_pairwise() mantel_between_blocks() mantel_block_vs_col(): Mantel test utilities for species-environment distance matrix correlation

Low-level correlation and network-inference functions powered by Rcpp. These are called internally by the builders but can also be used directly.

Extract, transform, reorder, and export graph components.

get_graph_nodes(): Extract node table from graph object
get_graph_adjacency(): Extract adjacency matrix from graph object
get_info_from_graph(): Extract node and edge information from graph object
get_subgraph(): Extract subgrah from graph object
order_graph(): Reorder the Modularity from graph object
update_graph_modules(): Update module names in an existing graph object
update_graph_modules2(): Update module assignments from an existing column in graph object
export_ggnetview(): Save a ggNetView with sensible defaults
trans_adjacency_matrix_to_df(): Trans adjacency matrix to edge data frame
trans_TOM_in_WGCNA(): Translate TOM matrin to create graph object
angle_utils: Angle helpers for ggNetView layout parameters
deg(): Convert degrees to radians

ggplot2 theme and colour/fill scale helpers for consistent network aesthetics.

Bundled example data used throughout the documentation, vignettes and \examples.

otu_tab: Example OTU abundance table
otu_rare: Rarefied OTU abundance table
otu_rare_relative: Relative-abundance OTU table
otu_sample: Sample metadata for the OTU example
tax_tab: Taxonomy annotation table
otu_NatureWater: Larger OTU table from a published water-quality study
tax_NatureWater: Taxonomy table for [otu_NatureWater]
BASV_tab: Bacterial ASV demonstration table
FASV_tab: Fungal ASV demonstration table
Spedf: Species composition table for link-heatmap examples
Envdf: Environmental variables (single block)
Envdf_4st: Environmental variables across four sampling stages
Envdf_4st_2: Alternative four-stage environmental dataset
adjacency_matrix_example: Pre-computed adjacency matrix
double_mat_node_df: Two-block node table for double-matrix examples
double_mat_node_df_with_modularity: Two-block node table with pre-computed modularity
ppi_example: Protein-protein interaction example
ppi_module: Protein-protein interaction example with module assignment