PlotPathNet {BioM2}

Network diagram of pathways-level features

Description

Network diagram of pathways-level features

Usage

PlotPathNet(
  data = NULL,
  BioM2_pathways_obj = NULL,
  FeatureAnno = NULL,
  pathlistDB = NULL,
  PathNames = NULL,
  cutoff = 0.2,
  num = 10
)

Arguments

data

The input omics data

BioM2_pathways_obj

Results produced by BioM2()

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") )

pathlistDB

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

PathNames

A vector.A vector containing the names of pathways

cutoff

Threshold for correlation between features within a pathway

num

The first few internal features of each pathway that are most relevant to the phenotype

Value

a ggplot object