pathwayResultsPlot: Cluster and plot significant pathways by FDR-adjusted pval

In ncats/RaMP-DB: RaMP (Relational Database of Metabolomic Pathways)

Cluster and plot significant pathways by FDR-adjusted pval

Description

Cluster and plot significant pathways by FDR-adjusted pval

Usage

pathwayResultsPlot(
  db = RaMP(),
  pathwaysSig,
  pval = "FDR",
  perc_analyte_overlap = 0.5,
  perc_pathway_overlap = 0.5,
  min_pathway_tocluster = 3,
  text_size = 8,
  sig_cutoff = 0.05,
  interactive = FALSE
)

Arguments

pathwaysSig	output of FilterFisherResults
pval	Which p value to plot, choose from Raw, FDR or Holm-adjusted
perc_analyte_overlap	Minimum overlap for pathways to be considered similar (Default = 0.2)
perc_pathway_overlap	Minimum overlap for clusters to merge (Default = 0.2)
min_pathway_tocluster	Minimum number of 'similar' pathways required to start a cluster (medoid) (Default = 3)
text_size	Scales all text in figure (Default=16)
sig_cutoff	Aesthetic, shows pvalue cutoff for significant pathways
interactive	If TRUE, return interactive plotly object instead of ggplot object

ncats/RaMP-DB documentation built on June 1, 2024, 9:34 p.m.