Description Usage Arguments Value Author(s) See Also Examples
In ProfilePlot
, the gene profiles of the significant genes for a specific
cluster are shown on 1 plot. Therefore, each gene is normalized by subtracting its
the mean.
1 2 3 4 |
Genes |
The genes to be plotted. |
Comps |
The objects to be plotted or to be separated from the other objects. |
GeneExpr |
The gene expression matrix or ExpressionSet of the objects. |
Raw |
Logical. Should raw p-values be plotted? |
OrderLab |
Optional. If the compounds are to set in a specific order of a specific method. |
ColorLab |
The clustering result that determines the color of the labels of the objects in the plot. |
nrclusters |
Optional. The number of clusters to cut the dendrogram in. |
cols |
Optional. The color to use for the objects in Clusters for each method. |
AddLegend |
Optional. Whether a legend of the colors should be added to the plot. |
margins |
Optional. Margins to be used for the plot. |
extra |
The space between the plot and the legend. |
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, i.e. no new device is opened and the plot appears in the current device or document. |
location |
If plottype is "pdf", a location should be provided in "location" and the figure is saved there. |
... |
Optional parameter to be handed to the plot function. |
A plot which contains multiple gene profiles. A distinction is made between the values for the objects in Comps and the others.
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 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 | ## Not run:
data(fingerprintMat)
data(targetMat)
data(geneMat)
data(GeneInfo)
data(ListGO)
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_Paths_FandT=PathwaysIter(L,GeneExpr=geneMat,nrclusters=7,method=c("limma", "MLP"),
GeneInfo=GeneInfo,geneSetSource = "GOBP",top=NULL,topG=NULL,GENESET=ListGO,sign=0.05,
niter=2,fusionsLog=TRUE,WeightClust=TRUE,names=c("FP","TP"))
MCF7_Paths_intersection=Geneset.intersect(MCF7_Paths_FandT,0.05,names=names,
seperatetables=FALSE,separatepvals=FALSE)
MCF7_DiffGenes_FandT10=DiffGenes(list(MCF7_F,MCF7_T),geneMat,nrclusters=7,"limma",0.05,top=10)
MCF7_Shared10=Shared(DataLimma=MCF7_DiffGenes_FandT10,DataMLP=MCF7_Paths_intersection)
Comps=SharedComps(list(MCF7_DiffGenes_FandT10$`Method 1`$"Cluster 1",
MCF7_DiffGenes_FandT10$`Method 2`$"Cluster 1"))
MCF7_SharedGenes=FindGenes(DataLimma=MCF7_DiffGenes_FandT10,names=c("FP","TP"))
Genes=names(MCF7_SharedGenes[[1]])[-c(2,4,5)]
ListC=list(MCF7_DiffGenes_FandT10[[1]][[1]]$Compounds$LeadCpds,
MCF7_DiffGenes_FandT10[[2]][[1]]$Compounds$LeadCpds)
colscl=ColorPalette(colors=c("red","green","purple","brown","blue","orange"),ncols=9)
ProfilePlot(Genes=Genes,Comps=Comps,GeneExpr=geneMat,Raw=FALSE,OrderLab=MCF7_F,
ColorLab=NULL,nrcluster=7,Clusters=ListC,cols=colscl,AddLegend=TRUE,
usedgenes=Genes,margins=c(8.1,4.1,1.1,6.5),plottype="new",location=NULL,cex=0.75)
## End(Not run)
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