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Subset Cnet igraph

Source: R/jamenrich-base.r
subsetCnetIgraph.Rd

Subset Cnet igraph

Usage

subsetCnetIgraph(
  gCnet,
  includeSets = NULL,
  includeGenes = NULL,
  remove_singlets = TRUE,
  minSetDegree = 1,
  minGeneDegree = 1,
  remove_blanks = FALSE,
  spread_labels = TRUE,
  force_relayout = TRUE,
  do_reorder = TRUE,
  repulse = 4,
  layout = NULL,
  verbose = FALSE,
  ...
)

Arguments

gCnet

igraph object representing Cnet concept network data

includeSets

character vector, or NULL, containing the set names or labels to retain.

includeGenes

character vector, or NULL, containing the gene names or labels to retain.

remove_singlets

logical whether to remove singlet graph nodes, which are nodes that have no remaining edges. Note that argument "removeSinglets" is deprecated but will be recognized with preference, support will be removed in future versions.

minSetDegree

integer value indicating the minimum number of edges each Set node must have to be retained in the resulting igraph. Use minSetDegree=2 to retain only Set nodes that have multiple connected Gene nodes.

minGeneDegree

integer value indicating the minimum number of edges each Gene node must have to be retained in the resulting igraph. Use minGeneDegree=2 to retain only Gene nodes that connect to multiple Set nodes.

remove_blanks

logical indicating whether to call removeIgraphBlanks(), which removes blank colors from "pie.color" and "coloredrect.color" attributes.

spread_labels

logical indicating whether to call spread_igraph_labels(), which re-orients the node labels after the igraph object has been subsetted. When TRUE, the arguments force_relayout, and do_reorder are passed to that function.

force_relayout

logical indicating whether to re-apply the igraph layout function.

do_reorder

logical indicating whether to call reorderIgraphNodes(), which sorts equivalent nodes by color then label, intended when there are large numbers of nodes with the same edges, typically most common in a cnet plot where many gene nodes may be connected to the same pathway set nodes.

layout

function that takes igraph object and returns a numeric matrix of node coordinates. This function is only called when force_relayout=TRUE, and must be supplied as a function in order to be applied properly to the subset Cnet igraph. To apply layout before the subset operation, do so with igraph::set_graph_attr(g, "layout", layout).

verbose

logical indicating whether to print verbose output.

...

additional arguments are ignored.

Details

This function produces a subset of a Cnet igraph based upon supplied set names or gene names. This function is intended to be a convenient method of filtering a Cnet igraph to a pre-defined set of "Set" names.

The function assumes graph nodes have an attribute "nodeType" with values either "Set" or "Gene" to indicate the type of node.

When includeSets is supplied, the graph is subsetted to include only nodes with nodeType="Set" with matching V(gCnet)$name or V(gCnet)$label. Then only neighboring nodes are retained, thus removing any nodes with nodeType="Gene" that do not connect to any of the given Set nodes. The result is a proper Cnet igraph that only contains Gene nodes connected to the subset of Set nodes.

If includeGenes is supplied, the graph is subsetted to include only nodes with nodeType="Gene" with matching V(gCnet)$name or V(gCnet)$label.

When removeSinglets=TRUE then any nodes that have no remaining edges are removed. Especially when supplying includeGenes, this option is useful to hide any Set nodes that have no connected Gene nodes.

See also

Other jam igraph functions: cnet2df(), cnet2im(), cnetplotJam(), cnetplot_internalJam(), color_edges_by_nodegroups(), color_edges_by_nodes(), color_edges_by_nodes_deprecated(), color_nodes_by_nodegroups(), communities2nodegroups(), drawEllipse(), edge_bundle_bipartite(), edge_bundle_nodegroups(), enrichMapJam(), fixSetLabels(), flip_edges(), get_bipartite_nodeset(), highlight_edges_by_node(), igraph2pieGraph(), jam_igraph(), jam_plot_igraph(), label_communities(), layout_with_qfr(), layout_with_qfrf(), mem2emap(), memIM2cnet(), mem_multienrichplot(), nodegroups2communities(), rectifyPiegraph(), relayout_with_qfr(), removeIgraphBlanks(), removeIgraphSinglets(), reorderIgraphNodes(), rotate_igraph_layout(), spread_igraph_labels(), subgraph_jam(), subset_igraph_components(), sync_igraph_communities(), with_qfr()