PlotGeneNetworks-PathwayObject-method: PlotGeneNetworks

In TranslationalBioinformaticsUnit/GeneSetCluster: Cluster together Gene-Sets from Gene Set Analysis

PlotGeneNetworks

Description

PlotGeneNetworks

Usage

## S4 method for signature 'PathwayObject'
PlotGeneNetworks(Object, labels = F,
  RRmin = 10)

Arguments

Object	a pathway object
labels	Boolean show labels or not, or a vector with labels to be shown
RRmin	filter for different RR cutoff for what is an edge.

Value

plot

Examples

IPA.files <- c(system.file("extdata", "MM10.IPA.KO.uGvsMac.Canonical_pathways.xls", package = "GeneSetCluster"),
              system.file("extdata", "MM10.IPA.WT.uGvsMac.Canonical_pathways.xls", package = "GeneSetCluster"),
              system.file("extdata", "MM10.IPA.KO.uGvsMac.Functional_annotations.xls",package = "GeneSetCluster"),
              system.file("extdata", "MM10.IPA.WT.uGvsMac.Functional_annotations.xls",
              package = "GeneSetCluster"))
canonical.files <- IPA.files[grep("Canonical", IPA.files)]

IPA.object1 <- LoadGeneSets(file_location = canonical.files, #where are  the files
                           groupnames= c("KO", "WT"),
                           P.cutoff = 1.3,
                           Mol.cutoff = 5,
                           Source = "IPA",
                           type = "Canonical_Pathways",
                           structure = "SYMBOL",
                           seperator = ",")
 IPA.object2 <- CombineGeneSets(Object = IPA.object1)
 IPA.object3 <- ClusterGeneSets(Object = IPA.object2,
                            clusters = 7,
                            method = "kmeans")

 PlotGeneNetworks(Object = IPA.object3, labels=F, RRmin = 0)

TranslationalBioinformaticsUnit/GeneSetCluster documentation built on Feb. 2, 2023, 4:06 a.m.