rotate_igraph_layout: Rotate igraph layout coordinates

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

Rotate igraph layout coordinates

Description

Rotate igraph layout coordinates, optionally after reflecting coordinates along one or more coordinate axes.

Usage

rotate_igraph_layout(
  g = NULL,
  degrees = 0,
  reflect = c("none", "x", "y", "z"),
  center = NULL,
  center_rule = c("median", "origin", "mean", "min", "max"),
  rotation_axes = c(1, 2),
  spread_labels = TRUE,
  do_reorder = FALSE,
  layout = NULL,
  verbose = FALSE,
  ...
)

Arguments

g	igraph object that contains layout coordinates in graph attributes, for example igraph::graph_attr(g, "layout").
degrees	numeric value indicating the degrees to rotate layout coordinates, where 360 degrees is one complete rotation.
reflect	character string indicating one or more axes to reflect coordinates, or "none" to reflect no axis.
center	numeric coordinates to use as the center, or center=NULL to calculate the center using center_rule.
center_rule	character string indicating which rule to apply to determine the center coordinates, when center=NULL: "origin" uses c(0, 0); "mean" uses the mean of each axis; "median" uses the median of each axis; "min" uses the minimum of each axis; "max" uses the max of each axis.
rotation_axes	integer vector indicating which axis coordinates to rotate, by default c(1, 2) uses the first two axes.
spread_labels, do_reorder	logical indicating whether to call spread_igraph_labels(), and subsequently whether to call reorderIgraphNodes().
layout	matrix with 2 or more columns, when defined this layout is used and not the layout from the g igraph object.
...	additional arguments are passed to spread_igraph_labels() which calls reorderIgraphNodes() when spread_labels=TRUE and do_reorder=TRUE, or to reorderIgraphNodes() when spread_labels=FALSE and do_reorder=TRUE. Notably, the optional argument sortAttributes can be passed through those functions to affect the node sort priority.

Details

This function rotates igraph layout coordinates by calling the function rotate_coordinates(). The input can either be g as igraph object, or layout as a numeric matrix.

Note that the reflect is applied before degrees. To change the order, call this function multiple times.

When both g and layout are supplied, the coordinates are used from layout, rotated, then stored in the g igraph object as a graph attribute, using igraph::graph_attr(g, "layout").

When only g is supplied, it is expected to contain layout coordinates in graph attributes, obtained with igraph::graph_attr(g, "layout").

When only layout is supplied, and no g igraph object is supplied, this function serves only as a wrapper to rotate_coordinates().

Rotation code kindly contributed by Don MacQueen to the maptools package, and is reproduced here to avoid a dependency on maptools and therefore the sp package.

This function also calls other useful helper functions, when spread_labels=TRUE it calls spread_igraph_labels() to position labels around each node based upon the angle of incoming edges, which has the effect of reducing label overlaps. When do_reorder=TRUE it calls reorderIgraphNodes() which sorts nodes within a nodeset by color then by label, to help visually group similar nodes together in equivalent positions in the layout.

Value

igraph when input g is supplied, otherwise ⁠numeric matrix⁠.

See Also

Other jam cnet igraph functions: adjust_cnet_nodeset(), adjust_cnet_set_relayout_gene(), apply_cnet_direction(), apply_nodeset_spacing(), get_cnet_nodeset(), make_cnet_test(), nudge_igraph_node()

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

Examples

layout <- cbind(0:10, 0:10);
layout_rot50 <- rotate_igraph_layout(layout=layout, degrees=50);
layout_rot40_ctrmean <- rotate_igraph_layout(layout=layout, degrees=40, center_rule="mean");
plot(rbind(layout, layout_rot50, layout_rot40_ctrmean),
   col=rep(c("darkorchid", "darkorange1", "dodgerblue"), each=11),
   pch=rep(c(17, 20, 18), each=11),
   cex=2);

if (require(igraph)) {
   g <- igraph::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);
   g <- relayout_with_qfr(g, repulse=8);
   g2 <- rotate_igraph_layout(g, degrees=45);
   opar <- par("mfrow"=c(1,2));
   on.exit(par(opar));
   jam_igraph(g,
      main="original layout",
      node_factor=0.6,
      label_dist_factor=7);
   jam_igraph(g2,
      main="rotated 45 degrees",
      node_factor=0.6,
      label_dist_factor=7);
}

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