jam_plot_igraph: Jam igraph vectorized plot function (internal)

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

Jam igraph vectorized plot function (internal)

Description

Jam igraph vectorized plot internal function called by jam_igraph()

Usage

jam_plot_igraph(
  x,
  ...,
  axes = FALSE,
  add = FALSE,
  xlim = NULL,
  ylim = NULL,
  mark.groups = list(),
  mark.shape = 1/2,
  mark.col = NULL,
  mark.alpha = 0.2,
  mark.border = NULL,
  mark.expand = 8,
  mark.lwd = 2,
  mark.lty = 1,
  mark.smooth = TRUE,
  mark.cex = 1,
  mark.x.nudge = 0,
  mark.y.nudge = 0,
  pie_to_jampie = TRUE,
  use_shadowText = FALSE,
  vectorized_node_shapes = TRUE,
  edge_bundling = c("default", "connections", "none", "mark.groups", "nodegroups"),
  bundle_self = FALSE,
  nodegroups = NULL,
  render_nodes = TRUE,
  render_edges = TRUE,
  render_groups = TRUE,
  render_nodelabels = TRUE,
  params = NULL,
  plot_grid = FALSE,
  verbose = FALSE,
  debug = NULL
)

Arguments

x	The graph to plot.
...	Additional plotting parameters. See igraph.plotting for the complete list.
axes	Logical, whether to plot axes, defaults to FALSE.
add	Logical scalar, whether to add the plot to the current device, or delete the device's current contents first.
xlim, ylim	default x and y axis limits. When either value is NULL the range is defined by the layout coordinate ranges, respectively, then expanded by adding expand to each side of the range.
mark.groups	A list of vertex id vectors. It is interpreted as a set of vertex groups. Each vertex group is highlighted, by plotting a colored smoothed polygon around and “under” it. See the arguments below to control the look of the polygons.
mark.shape	A numeric scalar or vector. Controls the smoothness of the vertex group marking polygons. This is basically the ‘shape’ parameter of the graphics::xspline() function, its possible values are between -1 and 1. If it is a vector, then a different value is used for the different vertex groups.
mark.col	A scalar or vector giving the colors of marking the polygons, in any format accepted by graphics::xspline(); e.g. numeric color ids, symbolic color names, or colors in RGB.
mark.alpha	numeric value between 0 (transparent) and 1 (opaque) indicating the transparency of mark.col color fill values, used only when mark.groups is defined, and mark.col is not defined.
mark.border	A scalar or vector giving the colors of the borders of the vertex group marking polygons. If it is NA, then no border is drawn.
mark.expand	A numeric scalar or vector, the size of the border around the marked vertex groups. It is in the same units as the vertex sizes. If a vector is given, then different values are used for the different vertex groups.
mark.lwd, mark.lty	line with and line type parameters for each mark.groups polygon.
mark.cex	numeric adjustment for mark label font size, used when mark.groups is supplied and has names(mark.groups).
mark.x.nudge, mark.y.nudge	numeric values in units of the maximum x-axis or y-axis range for the layout coordinates, used to adjust each label displayed when names(mark.groups) is defined. These arguments are passed to make_point_hull() as label.x.nudge, label.y.nudge, respectively.
pie_to_jampie	logical indicating whether to convert vertex shape "pie" to "jampie" in order to use vectorized plotting.
use_shadowText	logical indicating whether to use jamba::shadowText() instead of graphics::text(), in order to render text labels with a subtle shadow-like outline around each label. This change improves legibility of labels at the expense of slightly longer plot rendering time.
vectorized_node_shapes	logical indicating whether to plot vertex node shapes using vectorized operations. It is substantially faster, however the one drawback is that nodes are plotted in order of their shape, which affects the positioning of nodes when there are node overlaps. This tradeoff is relatively minor, and it is recommended either to reposition nodes to reduce or prevent overlaps, or adjust node sizes to reduce overlaps.
edge_bundling	character string or function, where: "default" will try to detect an appropriate method: when nodegroups or mark.groups are defined, it chooses the matching option (see below); otherwise it chooses "connections". "none" will perform no edge bundling. This method is best when rendering straight edges, or for rendering multiple identical edges with curvature as defined by igraph::igraph.plotting(). "connections" will perform graph edge bundling by shared connections by calling edge_bundle_bipartite() then edge_bundle_nodegroups(). This option is particularly good for bipartite graphs such as concept networks (cnet plots). "mark.groups" will perform graph edge bundling using mark.groups by calling edge_bundle_nodegroups(). This option is equivalent to "nodegroups" except that it uses mark.groups to define node groupings. "nodegroups" will perform graph edge bundling using nodegroups by calling edge_bundle_nodegroups(). This option is equivalent to "mark.groups" except that it uses nodegroups to define node groupings. function will call a custom edge bundling function using the igraph object x and the igraph parameters param as input. This output is currently untested, and is intended to enable alternative edge bundling functions which may exist outside this package. The custom function should be able to use the node layout coordinates in graph_attr(x, "layout"), and render edges between nodes.
nodegroups	list object as output by edge_bundle_bipartite() where each list element is a character vector of vertex node names present in igraph::V(x)$name. If no "name" vertex node attribute exists, then integer index values are used as names. Note that all vertex nodes must be represented in nodegroup in order for the corresponding edges to be plotted.
render_nodes, render_edges	logical indicating whether to render vertex nodes, or edges, respectively. Sometimes it can be useful to call this function for other byproduct outputs, for example, jam_plot_igraph(graph, add=FALSE, render_nodes=FALSE, render_edges=FALSE) will create a new plot device with appropriate axis ranges, and can be used to render edge bundling results for example.
render_groups	logical indicating whether to render groups when mark.groups is supplied. Groups are rendered with a shaded polygon and border.
render_nodelabels	logical indicating whether to draw node labels, which is typically the last operation in the plot sequence. Note that node labels can be rendered without also rendering the nodes or edges.
plot_grid	logical indicating whether to plot a background grid indicating units of 2% across the layout of the network graph. The units are calculated consistent with nudge_igraph_nodes(), adjust_cnet_nodeset() and other functions, scaled relative to the maximum x- or y-coordinate range of layout of the graph. Layout is obtained by get_igraph_layout() which by default uses supplied layout, or graph attribute igraph::graph_attr(x, "layout"). Note that by default, jam_igraph() represents the layout with aspect ratio = 1, so x-coordinates and y-coordiantes are represented with the same spacing per unit. This function calls plot_layout_scale() to render the grid lines.
verbose	logical indicating whether to print verbose output.
debug	logical or character vector of attributes for which debug output will be plotted onscreen.

Details

Note that this function is intended to be called by jam_igraph(), and is an internal function not intended to be called directly.

The jam_igraph() handles the overall plot equivalent of igraph::plot.igraph(), however it calculates layout coordinates, and defines more useful x- and y-axis ranges, and then adjusts node and label sizes relevant to the layout data range. Specifically vertex.size=15 is only useful when the layout range is rescaled between -1 and 1; however when using jam_igraph() the vertex is scaled relative to the actual layout ranges.

The steps here are a reproduction of igraph:::plot.igraph() with four changes:

1. Default rescale=FALSE, and asp=1 which means igraph layout is drawn true to the layout coordinates without distortion. To use default igraph::plot.igraph() behavior, use rescale=TRUE. The new default may not be appropriate for bipartite layout algorithms that generate two columns, and seems most useful with organic layouts where aspect ratio 1 helps convey important meaning in the graph structure, namely by enforcing consistent x- and y-axis visual distance between nodes.

   • Related: the xlim and ylim values are automatically adjusted to include the layout coordinate range. The default igraph::plot.igraph(..., rescale=FALSE) does not adjust the xlim and ylim ranges, which can be problematic when supplying layout as a function, and therefore the output node coordinates are not known until the plot rendering step.

When vectorized_node_shapes=TRUE by default:

1. When there are multiple different vertex "shape" attributes, the nodes are rendered vectorized one shape at a time. The original igraph::plot.igraph() draws each individual vertex one by one, which is substantially slower (minutes compared to 1-2 seconds) for large igraph objects.

2. When there are multiple font families, the default plot function draws each label one by one. The jam_plot_igraph() draws labels in groups of font family, in order to comply with limitations in graphics::text(). This situation is fairly rare, however the speed improvement is substantial, again roughly minutes down to 1-2 seconds.

The fourth difference involves edge bundling:

1. When edge_bundling is used, it renders edges differently than the approach in igraph::plot.igraph(), by drawing curved splines for each bundle of edges.

Some other distinctive features include:

When use_shadowText=TRUE node labels call jamba::shadowText() which draws a small partly transparent outline around labels, making them more legible when they overlap colored nodes. This step effectively draws each label n times, which can slightly slow the rendering of the overall figure.

When pie_to_jampie=TRUE, any nodes with shape="pie" are changed to shape="jampie" for the purpose of rendering pie shapes in vectorized fashion, instead of being drawn for each node separately. This change is a substantial improvement in rendering time.

Default colors for marked node groups mark.col and mark.border when not defined upfront, will call colorjam::rainbowJam() and not ⁠grDevices::rainbow(). The ⁠colorjam::rainbowJam()⁠produces more visually distinct categorical colors. This behavior can be controlled by supplying a⁠character⁠vector with specific colors for⁠mark.colandmark.border⁠. Note that the border should match the colors, or it can be set to ⁠"grey45"' for a generally visible border.

Optional argument nodegroups can be supplied, which is a list of vectors, where each vector represents a group of nodes. The nodegroups can be used with edge_bundling="nodegroups" to define custom edge bundling.

Finally, individual plot components can be individually disabled:

• render_nodes=FALSE

• render_edges=FALSE

• render_groups=FALSE

• render_nodelabels=FALSE

Note that this function is not called by default, and is only called by multienrichjam::jam_igraph().

All other arguments are documented in igraph::plot.igraph().

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(), 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()

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