IntClust (version 0.0.2)

PlotPathways: A GO plot of a pathway analysis output.

Description

The PlotPathways function takes an output of the PathwayAnalysis fucntion and plots a GO graph with the help of the plotGOgraph function of the MLP package.

Usage

PlotPathways(Pathways,nRow=5,main=NULL,plottype="new",location=NULL)

Arguments

Pathways

One element of the output list returned by PathwayAnalysis or Geneset.intersect.

nRow

Number of GO IDs for which to produce the plot

main

Title of the plot.

plottype

Should be one of "pdf","new" or "sweave". If "pdf", a location should be provided in "location" and the figure is saved there. If "new" a new graphic device is opened and if "sweave", the figure is made compatible to appear in a sweave or knitr document.

location

If plottype is "pdf", a location should be provided in "location" and the figure is saved there.

Value

The output is a GO graph.

Examples

# NOT RUN {
data(fingerprintMat)
data(targetMat)
data(geneMat)
data(GeneInfo)
data(GS)

MCF7_F = Cluster(fingerprintMat,type="data",distmeasure="tanimoto",normalize=FALSE,
method=NULL,clust="agnes",linkage="ward",gap=FALSE,maxK=55,StopRange=FALSE)
MCF7_T = Cluster(targetMat,type="data",distmeasure="tanimoto",normalize=FALSE,
method=NULL,clust="agnes",linkage="ward",gap=FALSE,maxK=55,StopRange=FALSE)

L=list(MCF7_F,MCF7_T)
names=c('FP','TP')

MCF7_PathsFandT=PathwayAnalysis(L, GeneExpr = geneMat, nrclusters = 7, method = c("limma", 
"MLP"), ENTREZID = GeneInfo[, 1], geneSetSource = "GOBP", topP = NULL, 
topG = NULL, GENESET = GS, sign = 0.05,niter=2,fusionsLog = TRUE, WeightClust = TRUE, 
 names =names,seperatetables=FALSE,separatepvals=FALSE)
 
PlotPathways(MCF7_PathsFandT$FP$Pathways,nRow=5,main=NULL)
# }