View source: R/plottingFunctions.R

pathwayResultsPlot | R Documentation |

Cluster and plot significant pathways by FDR-adjusted pval

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 )

`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 |

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