Nothing
pickWGCNAParam <-
function (DEGeneExpr,Alphas=c(c(1:10), seq(from = 12, to=20, by=2)),AThreshold=0.85,interactiveMode=T)
{
CorrelationVals<-computeSimilarities(DEGeneExpr)
Correlations<-CorrelationVals$Correlations
PValues<-CorrelationVals$PValues
Similarities<-CorrelationVals$Similarities
rm(CorrelationVals)
Adjacencies<-list()
for (Alpha in Alphas)
{
Adjacencies[[as.character(Alpha)]] = 1/(1+exp(-Alpha*(Similarities-0.5)))
}
PossibleColors=rainbow(length(Adjacencies))
names(PossibleColors)=names(Adjacencies)
NEdges=PValuesMax=ConnecMeans=MinRhos=vector()
for (Alpha in names(Adjacencies))
{
Abscissa="Similarity"
Ordinate="Adjacency"
Titre="Adjacency computation parameters"
if (Alpha!=names(Adjacencies)[1])
{
par(new=T)
Abscissa=""
Ordinate=""
Titre=""
}
Adjacency=Adjacencies[[Alpha]]
plot(c(Adjacency)~c(Similarities),bg=PossibleColors[Alpha],ylim=c(0,1),xlim=c(0,1),pch=21,col="black",main=Titre,xlab=Abscissa,ylab=Ordinate)
EdgesPos=which(Adjacency>AThreshold | Adjacency<(1-AThreshold))
NEdges=c(NEdges,length(EdgesPos)/2)
EdgesMatrix=matrix(0,ncol=ncol(Adjacency),nrow=nrow(Adjacency))
RhosMatrix=matrix(Inf,ncol=ncol(Correlations),nrow=nrow(Correlations))
colnames(EdgesMatrix)=colnames(RhosMatrix)=colnames(Adjacency)
rownames(EdgesMatrix)=rownames(RhosMatrix)=rownames(Adjacency)
if (length(EdgesPos) > 0)
{
ThresPos=which.min(abs(Adjacency-AThreshold))
PValuesMax=c(PValuesMax,PValues[ThresPos])
}
if (length(EdgesPos) == 0)
{
PValuesMax=c(PValuesMax,1)
}
EdgesMatrix[EdgesPos]=Adjacency[EdgesPos]
RhosMatrix[EdgesPos]=abs(Correlations[EdgesPos])
Connectivities=apply(EdgesMatrix,2,function(x){return(length(which(x!=0)))})
ConnecMeans=c(ConnecMeans,mean(Connectivities))
MinRhos=c(MinRhos,min(RhosMatrix[which(RhosMatrix!=0)]))
}
names(NEdges)=names(PValuesMax)=names(ConnecMeans)=names(MinRhos)=names(Adjacencies)
abline(h=AThreshold,lty=2,lwd=2)
abline(h=1-AThreshold,lty=2,lwd=2)
legend("topleft",legend=names(Adjacencies),pch=21,col="black",pt.bg=PossibleColors,ncol=3,bg="white",title="Alpha values")
interactivePrompt<-"Press return for next plot..."
if(interactiveMode){line <- readline(interactivePrompt)}
plot(NEdges~names(NEdges),type="n",xlab="Alpha",ylab="Edges number",main="Edges number as a function of Alpha")
text(names(NEdges),NEdges,names(NEdges),col="red",cex=2)
Percents=c(0.05,0.1,0.25)
abline(h=Percents*length(Correlations)/2,lty=2,lwd=2)
if(interactiveMode){line <- readline(interactivePrompt)}
plot(-log(PValuesMax,10)~names(PValuesMax),type="n",xlab="Alpha",ylab="-log10(max(P-Values))",main="Maximal P-Values as a function of Alpha")
text(names(PValuesMax),-log(PValuesMax,10),names(PValuesMax),col="red",cex=2)
PValsBreaks=c(0.05,0.01,0.001,0.0001)
abline(h=-log(PValsBreaks,10),lty=2,lwd=2)
if(interactiveMode){line <- readline(interactivePrompt)}
plot(ConnecMeans~names(ConnecMeans),type="n",xlab="Alpha",ylab="mean(Connectivities)",main="Connectivities as a function of Alpha")
text(names(ConnecMeans),ConnecMeans,names(ConnecMeans),col="red",cex=2)
if(interactiveMode){line <- readline(interactivePrompt)}
plot(MinRhos~names(MinRhos),type="n",xlab="Alpha",ylab="min(Rhos)",main="Minimal rhos as a function of Alpha")
text(names(MinRhos),MinRhos,names(MinRhos),col="red",cex=2)
RhosBreaks=c(0.4,0.45,0.6,0.8,0.85)
abline(h=RhosBreaks,lty=2,lwd=2)
if(interactiveMode){line <- readline(interactivePrompt)}
hist(abs(Correlations[upper.tri(Correlations)]),20,col="red",xlab="abs(Rho)",ylab="Frequency",main="Distribution of absolute values of Rho")
if(interactiveMode){line <- readline(interactivePrompt)}
hist(-log(PValues[upper.tri(PValues)],10),20,col="red",xlab="-log10(P-Value)",ylab="Frequency",main="Distribution of P-Values (log scale)")
abline(v=-log(0.05,10),lty=2,lwd=2)
if(interactiveMode){line <- readline(interactivePrompt)}
plot(-log(PValues[upper.tri(PValues)],10)~abs(Correlations[upper.tri(Correlations)]),pch=21,col="black",bg="red",xlab="abs(Rho)",ylab="-log10(P-Value)",main="P-Values as a function of Rhos")
abline(h=-log(0.05,10),lty=2,lwd=2)
RhoMin=abs(Correlations[which.min(abs(PValues-0.05))])
abline(v=RhoMin,lty=2,lwd=2)
if(interactiveMode){line <- readline("Press return to close the plot...");dev.off()}
}
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