cnet2df: Summarize Cnet igraph as a data.frame

In jmw86069/multienrichjam: Analysis and Visualization of Multiple Gene Set Enrichments

Summarize Cnet igraph as a data.frame

Description

Summarize Cnet igraph as a data.frame

Usage

cnet2df(g, getNeighbors = TRUE, checkSubsets = getNeighbors, ...)

Arguments

g	igraph object containing Cnet data, specifically vertex attribute name "nodeType" with values "Set" and "Gene", and where "Set" nodes are only connected to "Gene" nodes.
getNeighbors	logical indicating whether to include the connected neighbor node names.
checkSubsets	logical indicating whether to test "Set" nodes to determine if the neighbors are all represented by another "Set" node.
...	additional arguments are ignored.

Details

This function provides a data.frame summary of an igraph object containing "Cnet" data, including vertex attribute "nodeType" with values "Set" and "Gene", and where "Set" nodes are only connected to "Gene" nodes.

The data.frame is intended to provide a convenient method for subsetting nodes, typically based upon a connected cluster, or the minimum number of edges per node. For example, filter for the connected component containing a node of interest, or filter for "Set" nodes with more than one "Gene".

Value

data.frame with the node name, label, degree (number of edges), membership (based upon connected component), and if getNeighbors=TRUE it includes comma-delimited names of neighboring nodes.

See Also

Other jam igraph functions: cnet2im(), cnetplotJam(), cnetplot_internalJam(), color_edges_by_nodegroups(), color_edges_by_nodes_deprecated(), color_edges_by_nodes(), color_nodes_by_nodegroups(), communities2nodegroups(), drawEllipse(), edge_bundle_bipartite(), edge_bundle_nodegroups(), enrichMapJam(), fixSetLabels(), flip_edges(), get_bipartite_nodeset(), igraph2pieGraph(), jam_igraph(), jam_plot_igraph(), label_communities(), layout_with_qfrf(), layout_with_qfr(), mem2emap(), memIM2cnet(), mem_multienrichplot(), nodegroups2communities(), rectifyPiegraph(), relayout_with_qfr(), removeIgraphBlanks(), removeIgraphSinglets(), reorderIgraphNodes(), rotate_igraph_layout(), spread_igraph_labels(), subgraph_jam(), subsetCnetIgraph(), subset_igraph_components(), sync_igraph_communities(), with_qfr()

Other jam conversion functions: cnet2im(), enrichDF2enrichResult(), enrichList2IM(), enrichList2df(), enrichMapJam()

jmw86069/multienrichjam documentation built on Feb. 7, 2024, 12:58 a.m.