PlotPathways: A GO plot of a pathway analysis output.

In rforge/intclust: Integrated Data Analysis via Clustering

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.

Author(s)

Marijke Van Moerbeke

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)

## End(Not run)

rforge/intclust documentation built on Feb. 21, 2022, 7:47 a.m.