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Generate a plot for enrichment analysis of Canopus-predicted terms across multiple levels

CanopusListEnrichmentPlot_2.Rd

This function generates a plot for enrichment analysis of Canopus-predicted terms across multiple levels, showing fold enrichment, p-value, and subset count for each term level.

Usage

CanopusListEnrichmentPlot_2(
  mmo,
  id_list,
  pthr = 0.05,
  outdir,
  height = 5,
  width = 5,
  topn = 5,
  pval = "pval",
  save_output = TRUE
)

Arguments

mmo

The mmo object with sirius annotation and normalized data

id_list

A vector containing names of features to analyze

pthr

The threshold for adjusted p-value to be considered significant (default: 0.05)

outdir

The output file path for the enrichment plot

height

The height of the output plot in inches (default: 5)

width

The width of the output plot in inches (default: 5)

topn

The number of top terms to display in the plot (default: 5)

pval

pvalue options-pval or fdr (default: 'pval')

save_output

boolean, whether to save the output plot (default: TRUE)

Value

A list containing the enrichment plot and the enrichment results

Examples

if (FALSE) {
CanopusListEnrichmentPlot_2(
 mmo, id_list = DAMs_up$control_vs_treatment1.up,
 pthr = 0.05, outdir = 'canopus_enrichment_plot_topn.pdf',
 height = 5, width = 5, topn = 5
)
}