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Plot ComplexHeatmap

Source: R/plot_gene_geneset_ComplexHeatmap.R
plot_ComplexHeatmap.Rd

Plot ComplexHeatmap from enrichment analysis results and corresponding genelist

Usage

plot_ComplexHeatmap(
  enrichment_result,
  genelist,
  genes = NULL,
  cluster_method = "single",
  n_cluster = 1,
  n_top_terms = NA,
  n_top_genes = NA,
  genelist_overlap = NULL,
  plot = FALSE
)

Arguments

enrichment_result

dataframe containing enrichment analysis results. Must include name (gene set names) and symbol (listed genes associated with gene sets)

genelist

dataframe with gene-level statistics, including at least symbol, pvalue, effectsize, and signif columns

genes

character, default: NULL, if genes given, these are prioritized for visualization

cluster_method

default: 'single', else one of hclust methods

n_cluster

default: 1, integer, number of hierarchical clusters to define

n_top_terms

default: NULL, if integer, plot only top genesets (recommended for visual clarity: 70)

n_top_genes

default: NULL, if integer, plot only top genes (recommended for visual clarity: 150)

genelist_overlap

(Optional) dataframe with gene overlap information, including symbol and genelist_overlap, see run_genelists_overlap()

plot

default: FALSE, if TRUE, display drawn ComplexHeatmap

Value

A ComplexHeatmap object displaying genesets (rows) and genes (columns), potentially clustered based on their binary associations. The heatmap includes:

  • Row annotations: Gene set size, p-value, and average effect size.

  • Column annotations: Gene p-values, effect sizes, and optional overlap categories.

  • Customized row/column labels highlighting significant elements.

  • A color-mapped heatmap showing clustering results.

Examples

plot_ComplexHeatmap(
  get(load(system.file("extdata", "example_enrichment.rda", package = "goatea")))[seq.int(1, 3), ], 
  get(load(system.file("extdata", "example_genelist.rda", package = "goatea"))), 
  n_cluster = 3, 
  n_top_genes = 10
)