edge_bundle_nodegroups: Bundle edges using node groups

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

Bundle edges using node groups

Description

Bundle edges using node groups

Usage

edge_bundle_nodegroups(
  g,
  nodegroups,
  shape = NULL,
  params = NULL,
  midpoint = 0.5,
  detail = 10,
  draw_lines = TRUE,
  nodegroup_midpoints = NULL,
  linear_cor_threshold = 1,
  bundle_style = getOption("jam.bundle_style", "bezier"),
  bundle_self = FALSE,
  verbose = FALSE,
  debug = getOption("debug", FALSE),
  ...
)

Arguments

g	igraph that contains layout coordinates in graph attributes, stored as igraph::graph_attr(g, "layout").
nodegroups	list of node names, or object with class "communities" as produced by ⁠igraph::cluster_*⁠ methods such as igraph::cluster_walktrap(). Note that every node must be represented.
shape	character (optional) used to override the vertex.shape passed in params. It is recycled to the number of nodes, for example by igraph::vcount(g).
params	function representing igraph plotting parameters used at rendering time. The output is also produced by parse_igraph_plot_params() for use in jam_igraph() plotting, and is passed to other node and edge rendering functions.
midpoint	numeric vector of one or more values ranging from 0 to 1 that define control point positions along the line between two nodegroup center coordinates. When one nodegroup contains only one node, this line segment is shortened to end at that node border after clipping the corresponding node shape. The position along the line is defined relative to the first node in the edge, toward the second node in the edge. Using midpoint=0.5 guarantees the control point is the exact middle, while midpoint=c(0.2, 0.8) will use two control points at 20% and 80% distance along the line segment resulting in an edge that more closely follows the line segment.
detail	integer number of intermediate points along the spline to render for each edge.
draw_lines	logical indicating whether to render the edge splines after calculating them.
nodegroup_midpoints	list experimental support for defining specific control points used by bundled edges. Not fully implemented as yet. In future, it will require two nodegroups to be defined for each set of control point coordinates, with no requirement for the location of control points.
linear_cor_threshold	numeric value between 0 and 1. Coordinates for each edge, and intermediate control point coordinates are used in xspline() to create a curved spline from node to node. However, when the nodes and intermediate control points are already linear, the edge will be treated as a linear edge. To test for linearity, cor() correlation is calculated, and values at or above linear_cor_threshold are considered linear. The driving problem is when the control point is colinear with two nodes, and the control point is positioned outside the two nodes. Without this modification, the line would appear to pass from one node beyond the other node, with an arrow (if directed) pointing back to the other node from the opposite direction.
bundle_style	character string describing the type of curvature to use for edge bundles: "bezier": (default) calls bezier::bezier() to define a bezier curve using the edge control points. "xspline": calls graphics::xspline() to define an XSpline curve using the edge control points, however the method is customized to include each edge endpoint twice, which makes the intermediate curve much rounder than normal. "angular": calls graphics::xspline() to define an XSpline curve using the edge control points. This shape tends to appear angular, thus the name. "bezierPath": calls ggforce:::bezierPath() when ggforce is available, producing a bezier curve using the edge control points. Note this method appears identical to "bezier" above, and will likely be removed in a future release. "subway": experimental method that uses the "angular" appearance, with more repeated intermediate control points intended to group all bundled edges to the same linear segment. The intent is to "dodge" edges along the line segment, similar to the appearance of subway maps, however it is not fully implemented.
bundle_self	logical to indicate whether edges that begin and end in the same nodegroup should be bundled through the nodegroup center coordinate. bundle_self=FALSE forces all edges within a nodegroup to be rendered as straight lines, therefore not using the nodegroup center as the control point. bundle_self=TRUE overrides the validation check that requires the distance between center points of two nodegroups to have distance at least 0.5% the layout coordinate span. It can be a visual aid to have connections bundle through the center of the nodegroup, especially when the nodegroup is almost fully connected.
verbose	logical indicating whether to print verbose output.
debug	logical indicating whether to plot debug output that may be helpful in understanding the edge bundle control points. To specify debug only for edge bundling, use the substring "bundl", for example options("debug"="bundling").
...	additional arguments are ignored.

Details

This edge bundling technique relies upon some form of node grouping, usually derived from network community detection, or from bipartite nodesets (see get_bipartite_nodeset() for details.)

Given a set of node groups, edges are bundled entering and exiting each node group, along the linear path between the two node group center positions, using a spline function and intermediate control points.

The default spline uses the initial node positions, and the midpoint along the line between the two respective node groups. The midpoints can be adjusted with the argument midpoint and a vector of one or more fractional positions between 0 and 1. A useful alternative is midpoint=c(0.3, 0.7) which adds two control points along the linear path between node group centers, and tends to make the edges bundle closer together for a longer distance.

When used with bipartite nodesets, edges are bundled between each nodeset and individual nodes. The edge bundling rules are the same, with the default midpoint=c(0.4, 0.6) being centered at half the distance between the nodeset center, and the single node. In this case, the midpoint is directional, always pointing from the nodeset to the single node, therefore can be adjusted closer to the nodeset center with midpoint=0.2 or closer to the single node with midpoint=0.8.

Value

data.frame with each edge spline point represented on its own row, with breaks in edges defined by NA coordinates.

See Also

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(), 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()

Examples

# using community detection
karate <- igraph::make_graph("Zachary")
igraph::V(karate)$name <- as.character(seq_len(igraph::vcount(karate)))

# run any igraph::cluster_*()
wc <- igraph::cluster_louvain(karate)
# define list
nodegroups_wc <- split(igraph::V(karate)$name, wc$membership)

# bonus points for colorizing nodes and edges by community
igraph::V(karate)$color <- colorjam::group2colors(igraph::membership(wc));
igraph::V(karate)$label.color <- jamba::setTextContrastColor(igraph::V(karate)$color);
igraph::V(karate)$frame.color <- jamba::makeColorDarker(igraph::V(karate)$color);
karate <- color_edges_by_nodes(karate);

# update graph layout
layout_xy <- igraph::layout_with_graphopt(karate);
igraph::graph_attr(karate, "layout") <- layout_xy;

jam_igraph(karate,
   edge_bundling="nodegroups",
   nodegroups=nodegroups_wc,
   use_shadowText=TRUE);

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