BioM2 (version 1.1.0)

PlotPathFearture: 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
)

Value

a ggplot2 object

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