PlotGeneSets-PathwayObject-method: PlotGeneSets

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

PlotGeneSets

Description

PlotGeneSets

Usage

## S4 method for signature 'PathwayObject'
PlotGeneSets(Object, fontsize = 5,
  legend = T, annotation.mol = F, main = "", RR.max = "",
  cluster.order = "")

Arguments

Object	a PathwayObject
fontsize	a numeric with the fontsize for plotting
legend	add a legend to the plot
annotation.mol	should the genes from the genes set be added to the plot.
main	is the plot title
RR.max	is the maximum distance size to be added, it cutsoff the max to this. Usefull if the distance score gets very high.
cluster.order	is a user defined order of the clusters in the heatmap.
PathwayObject	a PathwayObject

Value

plot

Examples

Great.files <- c(system.file("extdata", "MM10.GREAT.KO.uGvsMac.bed.tsv",
                             package = "GeneSetCluster"),
system.file("extdata", "MM10.GREAT.KO.uGvsMac.bed_BCKGRND.tsv", package = "GeneSetCluster"),
system.file("extdata", "MM10.GREAT.WT.uGvsMac.bed.tsv", package = "GeneSetCluster"),
system.file("extdata", "MM10.GREAT.WT.uGvsMac.bed_BCKGRND.tsv", package = "GeneSetCluster"))
Great.files.bckgrnd <- Great.files[grepl("BCKGRND", Great.files)]


Great.bckgnrd.Object1 <- LoadGeneSets(file_location = Great.files.bckgrnd,
                                      groupnames= c("KO", "WT"),
                                      P.cutoff = 0.05,
                                      Mol.cutoff = 5,
                                      Source = "Great",
                                      Great.Background = TRUE,
                                      type = "Canonical_Pathways",
                                    topranks = 20,
                                   structure = "SYMBOL",
                                   Organism = "org.Mm.eg.db",
                                   seperator = ",")
man.Great.Object1 <- ManageGeneSets(Object = Great.bckgnrd.Object1,
                                   keep.type =c("Disease Ontology",
                                   "GO Biological Process" ),
                                   exclude.type="")
man.Great.Object2 <- CombineGeneSets(Object = man.Great.Object1)
man.Great.Object3 <- ClusterGeneSets(Object = man.Great.Object2,
                                     clusters = 5,
                                     method = "kmeans")
 PlotGeneSets(Object = man.Great.Object3, fontsize =5,
              legend = TRUE,
              annotation.mol=FALSE,
              main="man.Great.Object3",
              RR.max = 50)

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