Plot a Pathway Summary — plot_pathway_summary • microbiomedataset

Visualize pathway-level mechanism summaries as a ranked bar chart.

Usage

plot_pathway_summary(
  object,
  taxon_pathway_link = NULL,
  value = c("max_mechanism_score", "mean_mechanism_score", "n_taxa", "n_metabolites"),
  top_n = 15
)

Arguments

object: A crossomics_mechanism object or a pathway summary table.
taxon_pathway_link: Optional taxon-to-pathway link table used when object is a mechanism result.
value: Summary metric to display.
top_n: Maximum number of pathways displayed.

Value

A ggplot object.

Examples

data("demo_crossomics", package = "microbiomedataset")

association <- calculate_correlation(
  microbiome_data = demo_crossomics$microbiome_data,
  metabolome_data = demo_crossomics$metabolome_data,
  sample_link = demo_crossomics$sample_link,
  microbiome_rank = "Genus",
  metabolome_transform = "none"
)
pathway_link <- standardize_pathway_link(
  data.frame(
    taxon_id = summarise_taxa(
      demo_crossomics$microbiome_data,
      taxonomic_rank = "Genus"
    )@variable_info$variable_id[1],
    metabolite_id = demo_crossomics$metabolome_data@annotation_table$variable_id[1],
    pathway_id = "pathway_a",
    pathway_name = "Pathway A",
    stringsAsFactors = FALSE
  )
)
mechanism <- infer_metabolic_link(
  microbiome_data = demo_crossomics$microbiome_data,
  metabolome_data = demo_crossomics$metabolome_data,
  sample_link = demo_crossomics$sample_link,
  pathway_link = pathway_link,
  association_result = association,
  microbiome_rank = "Genus",
  q_value_cutoff = 1
)
plot_pathway_summary(mechanism, top_n = 10)