PlotPathFearture: Visualisation of significant pathway-level features

In BioM2: Biologically Explainable Machine Learning Framework

Visualisation of significant pathway-level features

Description

Visualisation of significant pathway-level features

Usage

PlotPathFearture(
  BioM2_pathways_obj = NULL,
  pathlistDB = NULL,
  top = 10,
  p.adjust.method = "none",
  begin = 0.1,
  end = 0.9,
  alpha = 0.9,
  option = "C",
  seq = 1
)

Arguments

BioM2_pathways_obj	Results produced by BioM2(,target='pathways')
pathlistDB	A list of pathways with pathway IDs and their corresponding genes ('entrezID' is used). For details, please refer to ( data("GO2ALLEGS_BP") )
top	Number of significant pathway-level features visualised
p.adjust.method	p-value adjustment method.(holm", "hochberg", "hommel", "bonferroni", "BH", "BY","fdr","none")
begin	The (corrected) hue in (0,1) at which the color map begins. Detail for scale_fill_viridis().
end	The (corrected) hue in (0,1) at which the color map ends. Detail for scale_fill_viridis()
alpha	The alpha transparency, a number in (0,1). Detail for scale_fill_viridis()
option	A character string indicating the color map option to use. Detail for scale_fill_viridis()
seq	Interval of x-coordinate

Value

a ggplot2 object

BioM2 documentation built on Aug. 8, 2025, 6:35 p.m.