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

View source: R/plottingFunctions.R

pathwayResultsPlotR Documentation

Cluster and plot significant pathways by FDR-adjusted pval

Description

Cluster and plot significant pathways by FDR-adjusted pval

Usage

pathwayResultsPlot(
  pathwaysSig,
  pval = "FDR",
  perc_analyte_overlap = 0.2,
  perc_pathway_overlap = 0.2,
  min_pathway_tocluster = 3,
  text_size = 16,
  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 Sept. 26, 2022, 4:37 a.m.