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Plot Enrichment Results from ExpOmicSet

Source: R/plot_enrichment.R
plot_enrichment.Rd

Visualize enrichment results stored in a MultiAssayExperiment (ExpOmicSet) object. Supports dotplots, heatmaps, cnetplots, networks, and multi-panel summary plots.

Usage

plot_enrichment(
  expomicset,
  feature_type = c("degs", "degs_robust", "omics", "factor_features", "degs_cor",
    "omics_cor", "factor_features_cor"),
  plot_type = c("dotplot", "cnet", "network", "heatmap", "summary"),
  top_n = 5,
  n_per_group = 5,
  add_top_genes = TRUE,
  top_n_genes = 5,
  heatmap_fill = TRUE,
  logfc_thresh = log2(1),
  pval_col = "P.Value",
  pval_thresh = 0.05,
  score_metric = "stability_score",
  score_thresh = NULL,
  overlap_thresh = 0.2,
  node_radius = 0.2,
  pie_colors = NULL,
  label_top_n = NULL,
  label_colour = "black",
  net_facet_by = NULL,
  max_terms = 30,
  node_size = 1,
  term_node_correction = 0.2,
  gene_node_correction = 3,
  go_groups = NULL,
  layout_algo = "fr",
  edge_alpha = 0.3,
  label_size = 3,
  feature_col = "feature",
  logfc_col = "logFC"
)

Arguments

expomicset

A MultiAssayExperiment object with enrichment results added via run_enrichment().

feature_type

Character; one of "degs", "degs_robust", "omics", "factor_features", "degs_cor", "omics_cor", or "factor_features_cor". Defines which enrichment results to use.

plot_type

Type of plot to generate. One of "dotplot", "cnet", "network", "heatmap", or "summary".

top_n

Integer; number of top go_groups to include (used in "dotplot"). Default is 5.

n_per_group

Integer; number of terms per group to plot (used in "dotplot"). Default is 5.

add_top_genes

Logical; if TRUE, appends top shared genes to dotplot facets. Default is TRUE.

top_n_genes

Integer; number of top genes to show in each group (used in "dotplot"). Default is 5.

heatmap_fill

Logical; whether to fill tiles by logFC in the heatmap. Default is TRUE.

logfc_thresh

Numeric; log2 fold change threshold for filtering (heatmap only). Default is log2(1).

pval_col

Column name of the p-value used for filtering in "degs" heatmap. Default is "P.Value".

pval_thresh

Threshold for pval_col (heatmap only). Default is 0.05.

score_metric

Column for stability score (used in "degs_robust" heatmap). Default is "stability_score".

score_thresh

Numeric; threshold for score_metric (heatmap only). Default is NULL.

overlap_thresh

Numeric; Jaccard threshold for edges in the network plot. Default is 0.2.

node_radius

Numeric; node size in network plot. Default is 0.2.

pie_colors

Optional named vector of colors for pie charts (network and cnet).

label_top_n

Integer; number of top nodes to label in network. Default is NULL.

label_colour

Color of node labels in network. Default is "black".

net_facet_by

Column used to facet the network plot (e.g., "category"). Default is NULL.

max_terms

Integer; max number of terms to include in the cnet plot. Default is 30.

node_size

Numeric; base node size for cnet plot. Default is 1.

term_node_correction

Scaling factor for term nodes in cnet plot. Default is 0.2.

gene_node_correction

Scaling factor for gene nodes in cnet plot. Default is 3.

go_groups

Optional character vector of GO group names to subset enrichment results (all plots).

layout_algo

Graph layout algorithm to use in "network" and "cnet" plots. Default is "fr".

edge_alpha

Transparency of network/cnet plot edges. Default is 0.3.

label_size

Font size for labels in network and cnet plots. Default is 3.

feature_col

Column name used to join gene-level metadata. Default is "feature".

logfc_col

Column name used for log2 fold change values. Default is "logFC".

Value

A ggplot or patchwork object corresponding to the requested plot type.

Details

This function visualizes results from run_enrichment() using one of several plot types:

  • "dotplot": Enrichment terms grouped by GO group, colored by significance.

  • "heatmap": Term–gene matrix with optional logFC fill and shared gene highlighting.

  • "network": Graph of term overlap based on shared genes, faceted by metadata if desired.

  • "cnet": Gene–term bipartite graph with gene logFC values and term pie slices.

  • "summary": Multi-panel figure with GO group ridgeplots, gene counts, and Venn diagram.

Examples

if (FALSE) { # \dontrun{
# Dotplot of top GO groups
plot_enrichment(expomicset, feature_type = "degs", plot_type = "dotplot")

# Heatmap for selected groups
plot_enrichment(expomicset, feature_type = "degs_robust", plot_type = "heatmap",
                go_groups = c("Group_1", "Group_2"))

# Gene-term cnetplot
plot_enrichment(expomicset, feature_type = "degs", plot_type = "cnet")

# Summary multi-panel
plot_enrichment(expomicset, feature_type = "degs", plot_type = "summary")
} # }