mem_multienrichplot: MultiEnrichMap plot
In jmw86069/jamenrich: Analysis and Visualization of Multiple Gene Set Enrichments

mem_multienrichplot

R Documentation

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.

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()