mem_multienrichplot: MultiEnrichMap plot

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

MultiEnrichMap plot

Description

MultiEnrichMap plot

Usage

mem_multienrichplot(
  mem,
  overlap = 0.1,
  overlap_count = 2,
  do_plot = TRUE,
  do_legend = TRUE,
  remove_blanks = TRUE,
  remove_singlets = TRUE,
  spread_labels = TRUE,
  y_bias = 1,
  label_edges = c("overlap_count", "count", "overlap", "label", "none"),
  edge_cex = 1,
  node_cex = 0.8,
  node_size = 5,
  edge_color = "#55555588",
  frame_color = "#55555500",
  shape = "pie",
  repulse = 3.7,
  sets = NULL,
  rescale = TRUE,
  edge_bundling = "connections",
  main = "MultiEnrichMap\noverlap >= {overlap}, overlap_count >= {overlap_count}",
  ...
)

Arguments

mem	list object output from multiEnrichMap(), specifically containing elements ⁠"multiEnrichMap","multiEnrichMap2"⁠ which are expected to be igraph objects.
overlap	numeric value between 0 and 1, indicating the Jaccard overlap filter to use for edge nodes. The value is used to delete edges whose values E(g)$overlap are below this threshold.
overlap_count	numeric value indicating the minimum overlap count below which edges are removed. The value E(g)$overlap_count is used for this filter.
do_plot	logical indicating whether to plot the final result.
do_legend	logical indicating whether to print a color legend, valid when do_plot=TRUE. Arguments ... are also passed to mem_legend(), for example x="bottomleft" can be overriden.
remove_blanks	logical indicating whether to call removeIgraphBlanks() which removes blank/empty colors in igraph nodes.
remove_singlets	logical indicating whether to remove singlet nodes, which are nodes that have no connections to other nodes. By default, singlets are removed, in order to help visualize the node connections that remain after filtering by overlap.
spread_labels	logical indicating whether to call spread_igraph_labels(), which places node labels at an angle offset from the node, in order to improve default label positions.
y_bias	numeric value passed to spread_igraph_labels() when spread_labels=TRUE.
repulse	numeric value used for network layout when layout_with_qfrf() is used.
sets	optional character vector of enriched sets to include, all other sets will be excluded. These values are matched with V(g)$name.
rescale	logical indicating whether the igraph layout coordinates are scaled to range c(-1, 1) before plotting. In practice, when rescale=FALSE the function jam_igraph() is called because it does much better at properly handling other settings during the change. The effect is mainly to keep layout aspect intact, in cases where the x- and y-axis ranges are not roughly the same size, for example a short-wide layout.
main	character string used as the title when do_plot=TRUE. This character string is passed to glue::glue() in order to include certain argument values such as overlap.
...	additional arguments are passed to removeIgraphBlanks(), removeIgraphSinglets(), and spread_igraph_labels() as needed.

Details

This function is likely to be replaced by mem2emap().

This function takes output from multiEnrichMap() and produces customized "multiple enrichMap" plots using an igraph network. It differs from the data provided from multiEnrichMap() mostly by enabling different overlap filters, and by automating several steps that help with network layout, and node label placement.

For the most flexible exploration of data, run multiEnrichMap() using a lenient overlapThreshold, for example overlapThreshold=0.1. Then call this function with increasing overlap until the visualization has insightful structure.

Value

invisibly returns the igraph object used for plotting, a by-product of this function when do_plot=TRUE is that the igraph object is also visualized. All custom plot elements are updated in the igraph object, so in principle a simple call to plot(...) should suffice.

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(), 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()

Other jam plot functions: adjust_polygon_border(), grid_with_title(), jam_igraph(), mem_enrichment_heatmap(), mem_gene_path_heatmap(), mem_legend(), mem_plot_folio(), plot_layout_scale()

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