plotPathwayResults: 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

plotPathwayResults(
  pathwaysSig,
  pVal = "FDR",
  percAnalyteOverlap = 0.5,
  percPathwayOverlap = 0.5,
  minPathwayToCluster = 3,
  textSize = 8,
  sigCutoff = 0.05,
  interactive = FALSE,
  db = RaMP()
)

Arguments

pathwaysSig	output of FilterFishersResults
pVal	Which p value to plot, choose from Raw, FDR or Holm-adjusted
percAnalyteOverlap	Minimum overlap for pathways to be considered similar (Default = 0.2)
percPathwayOverlap	Minimum overlap for clusters to merge (Default = 0.2)
minPathwayToCluster	Minimum number of 'similar' pathways required to start a cluster (medoid) (Default = 3)
textSize	Scales all text in figure (Default=16)
sigCutoff	Aesthetic, shows pvalue cutoff for significant pathways
interactive	If TRUE, return interactive plotly object instead of ggplot object
db	a RaMP database object

Examples

## Not run: 
plotPathwayResults(pathwaysSig = filtered.fisher.results, textSize = 8, percAnalyteOverlap = 0.2,
   minPathwayToCluster = 2, percPathwayOverlap = 0.2, interactive = FALSE, db = rampDB )

## End(Not run)

ncats/RaMP-DB documentation built on June 10, 2025, 10:50 a.m.