layout_with_qfr: igraph layout using qgraph Fruchterman-Reingold

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

igraph layout using qgraph Fruchterman-Reingold

Description

igraph layout using qgraph Fruchterman-Reingold

Usage

layout_with_qfr(
  g,
  repulse = 3.5,
  area = 8 * (igraph::vcount(g)^2),
  repulse.rad = (igraph::vcount(g)^repulse),
  constraints = NULL,
  constrain = NULL,
  seed = 123,
  weights = NULL,
  niter = NULL,
  max.delta = NULL,
  cool.exp = NULL,
  init = NULL,
  groups = NULL,
  rotation = NULL,
  layout.control = 0.5,
  round = TRUE,
  digits = NULL,
  verbose = FALSE,
  ...
)

Arguments

g	igraph object
repulse	exponent power used to scale the radius effect around each vertex. The default is slightly higher than the cube of the number of vertices, but as the number of vertices increases, values from 3.5 to 4 and higher are more effective for layout.
area	The area of the plot, default is the square of the number of vertices times 8. Changes to plot area will also affect values of repulse and repulse.rad.
repulse.rad	Repulse radius, defaults to the the number of vertices raised to the repulse power.
constraints	optional two-column matrix with the coordinates of nodes which should not be modified, and NA values for nodes where the position can be modified.
constrain	character optional vector of node names that should be constrained. This argument is a convenient shortcut for defining constraints, which is a layout coordinate matrix with NA values on each row where the coordinate is free to move, and numeric values where the coordinate is fixed. For graph g that contains layout in igraph::graph_attr(g, "layout"), the init can be defined with this layout, then constraints is defined using constrain.
...	other arguments are sent to qgraph::qgraph.layout.fruchtermanreingold()

Details

This function provides Fruchterman-Reingold layout for an igraph object using the implementation from the qgraph package, which provides important configuration options deprecated in the igraph implementation. Notably, the repulse.rad parameter is helpful in adjusting the relative spacing of vertices, where higher values cause tighter packing of vertices, and lower values allows greater spacing between vertices.

Value

two-column numeric matrix with coordinates for each vertex.

See Also

qgraph::qgraph.layout.fruchtermanreingold()

Other jam igraph functions: cnet2df(), 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(), 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()

Examples

if (suppressPackageStartupMessages(require(igraph))) {
g  <- make_graph( ~ A-B-C-D-A, E-A:B:C:D,
   F-G-H-I-F, J-F:G:H:I,
   K-L-M-N-K, O-K:L:M:N,
   P-Q-R-S-P, T-P:Q:R:S,
   B-F, E-J, C-I, L-T, O-T, M-S,
   C-P, C-L, I-L, I-P)

par("mfrow"=c(2,2));
plot(g, main="default layout\n(igraph)");

plot(g, main="layout_with_fr\n(igraph)", layout=layout_with_fr);

plot(g, main="layout_with_qfr\n(qgraph default)", layout=layout_with_qfr);

plot(g, main="layout_with_qfr, repulse=6\n(qgraph custom)",
   layout=function(g)layout_with_qfr(g, repulse=6));
}

jmw86069/multienrichjam documentation built on Nov. 3, 2024, 10:29 p.m.