Package index • ggNetView

All functions

BASV_tab: Bacterial ASV demonstration table
Envdf: Environmental variables (single block)
Envdf_4st: Environmental variables across four sampling stages
Envdf_4st_2: Alternative four-stage environmental dataset
FASV_tab: Fungal ASV demonstration table
Spedf: Species composition table for link-heatmap examples
adjacency_matrix_example: Pre-computed adjacency matrix
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_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_enrichGO(): Build a graph object from GO enrichment analysis
build_graph_from_igraph(): Build a graph object from a graph object
build_graph_from_mat(): Build a correlation-based network from a matrix
build_graph_from_module(): Build a graph object from a data frame and module Info
build_graph_from_multi_mat(): Build a graph object from multiple numeric matrices
build_graph_from_pie(): Build a pie graph object from a data frame
build_graph_from_wgcna(): Build a graph object from WGCNA result
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
export_ggnetview(): Save a ggNetView with sensible defaults
get_graph_adjacency(): Extract adjacency matrix from graph object
get_graph_nodes(): Extract node table from graph object
get_info_from_graph(): Extract node and edge information from graph object
get_network_topology(): Create network topology
get_network_topology_parallel(): Create network topology in parallel
get_palette(): Generate a named color palette for discrete classes
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_subgraph(): Extract subgrah from graph object
ggNetView(): Visualize a network with custom layouts
ggNetView_RMT(): One-shot, non-interactive RMT threshold scan with auto selection
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_heatmap_triple(): Visualize multi-orientation environmental-species correlation heatmaps2
gglink_heatmaps(): Visualize multi-orientation environmental-species correlation heatmaps
gglink_heatmaps_2(): Visualize multi-orientation environmental-species correlation heatmaps (adaptive sizing)
ggnetview_modularity_heatmaps(): Visualize network with module-environment heatmaps
ggnetview_zipi(): Compute Zi-Pi (within-module connectivity and participation coefficient)
mantel_pairwise() mantel_between_blocks(): Mantel test utilities for species-environment distance matrix correlation
order_graph(): Reorder the Modularity from graph object
otu_NatureWater: Larger OTU table from a published water-quality study
otu_rare: Rarefied OTU abundance table
otu_rare_relative: Relative-abundance OTU table
otu_sample: Sample metadata for the OTU example
otu_tab: Example OTU abundance table
ppi_example: Protein-protein interaction example
ppi_module: Protein-protein interaction example with module assignment
scale_color_ggnetview(): Custom discrete color scale for ggNetView
scale_fill_ggnetview(): Custom discrete fill scale for ggNetView
sparcc_matrix_rcpp(): SparCC correlation matrix (Rcpp implementation)
sparcc_pvalue_rcpp(): SparCC p-value matrix (Rcpp implementation)
spieceasi_matrix_rcpp(): SPIEC-EASI matrix (Rcpp implementation)
tax_NatureWater: Taxonomy table for [otu_NatureWater]
tax_tab: Taxonomy annotation table
theme_ggnetview(): ggNetView Theme
trans_TOM_in_WGCNA(): Translate TOM matrin to create graph object
trans_adjacency_matrix_to_df(): Trans adjacency matrix to edge data frame
update_graph_modules(): Update module names in an existing graph object
update_graph_modules2(): Update module assignments from an existing column in graph object