PlotPathInner {BioM2}

Visualisation Original features that make up the pathway

Description

Visualisation Original features that make up the pathway

Usage

PlotPathInner(
  data = NULL,
  pathlistDB = NULL,
  FeatureAnno = NULL,
  PathNames = NULL,
  p.adjust.method = "none",
  save_pdf = FALSE,
  alpha = 1,
  cols = NULL
)

Arguments

data

The input omics data

pathlistDB

A list of pathways with pathway IDs and their corresponding genes ('entrezID' is used). For details, please refer to ( data("GO2ALLEGS_BP") )

FeatureAnno

The annotation data stored in a data.frame for probe mapping. It must have at least two columns named 'ID' and 'entrezID'. (For details, please refer to data( data("MethylAnno") )

PathNames

A vector.A vector containing the names of pathways

p.adjust.method

p-value adjustment method.(holm", "hochberg", "hommel", "bonferroni", "BH", "BY","fdr","none")

save_pdf

Whether to save images in PDF format

alpha

The alpha transparency, a number in (0,1).

cols

palette (vector of colour names)

Value

a plot object