spread_igraph_labels: Spread igraph node labels by angle from node center

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

Spread igraph node labels by angle from node center

Description

Spread igraph node labels by angle from node center

Usage

spread_igraph_labels(
  g,
  layout = NULL,
  y_bias = 1,
  update_g_coords = TRUE,
  do_reorder = TRUE,
  sortAttributes = NULL,
  nodeSortBy = c("x", "-y"),
  repulse = 3.5,
  force_relayout = FALSE,
  label_min_dist = 0.5,
  verbose = FALSE,
  ...
)

Arguments

g	igraph object
layout	numeric matrix representing the x and y coordinates of each node in g, in the same order as V(g). When layout is not supplied, nodes are checked for attributes c("x", "y") which define a fixed internal layout. When force_layout=TRUE these coordinates are ignored. If that is not supplied, then layout_with_qfr() is called along with the repulse argument. Subsequent coordinates are stored in V(g)$x and V(g)$y when argument update_g_coords=TRUE.
y_bias	numeric value indicating the tendency to spread labels on the y-axis rather than symmetrically around each node. This argument elongates the circle surrounding a node into an ellipse with this ratio.
update_g_coords	logical indicating whether the layout coordinates will be stored in graph_attr(g, "layout").
do_reorder	logical indicating whether to call reorderIgraphNodes() which re-distributes equivalent nodes based upon the node color(s). A node is "equivalent" to another node if both nodes have identical edges.
sortAttributes, nodeSortBy	arguments passed to reorderIgraphNodes() when do_reorder=TRUE.
repulse	argument passed to layout_with_qfr() only when layout is not supplied, and the layout is not stored in c(V(g)$x, V(g)$y).
force_relayout	logical indicating whether the igraph layout should be recalculated, in order to override coordinates that may be previously stored in the igraph object itself. Note that when layout is supplied, it is always used.
label_min_dist	numeric value used to ensure all labels are at least some distance from the center. These units are defined by igraph, and are roughly in units of one line height of text.
...	additional arguments are passed to layout_with_qfr() when needed.

Details

This function uses the igraph vertex attribute "label.degree", which describes the angular offset for each vertex label. (The "label.degree" values are represented as radians, not degrees, starting at 0 for right, and proceeding clockwise starting from the right, down, left, top, right.)

This function requires a network layout, which must be fixed in order for the vertex labels to be properly oriented. Labels are oriented opposite the most dominant angular mean of edges from each network node. Typically the side of a node with the fewest edges has the most space to place a label. No further checks are performed for overlapping labels.

Note that this function only modifies the other important attribute "label.dist" when 'label_min_dist“ is defined, in order to enforce a minimum label distance from the center of each node. There is no other logic to position small or large labels to avoid overlapping labels.

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(), 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(), subgraph_jam(), subsetCnetIgraph(), subset_igraph_components(), sync_igraph_communities(), with_qfr()

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