Description Usage Arguments Value Author(s) Examples
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.
1 | PlotPathways(Pathways,nRow=5,main=NULL,plottype="new",location=NULL)
|
Pathways |
One element of the output list returned by |
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. |
The output is a GO graph.
Marijke Van Moerbeke
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ## 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)
|
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