Nothing
plotSuper <- function(x, data, BiclustSet){
superBiclusterSamples <- c()
superBiclusterGenes <- c()
iGroupColumns <- BiclustSet@ColumnMembership[x, ]
iGroupRows <- BiclustSet@GenesMembership[, x]
superBiclusterSamples <- as.logical(colSums(iGroupColumns) == nrow(iGroupColumns))
superBiclusterGenes <- as.logical(rowSums(iGroupRows) == ncol(iGroupRows))
plotProfilesWithinBicluster(x = data[superBiclusterGenes, superBiclusterSamples],
sampleNames = colnames(data)[superBiclusterSamples],
main = "gene profiles")
return(new("Biclust", Number=1, RowxNumber=matrix(superBiclusterGenes, ncol=1), NumberxCol=matrix(superBiclusterSamples, nrow=1),
info = list(Call="super bicluster",size = length(x)),
Parameters = list(Call=paste("Obtained from ",length(x),"biclusters" )) ))
}
plotSuperAll <- function(x, data, BiclustSet){
superBiclusterSamples <- c()
superBiclusterGenes <- c()
iGroupColumns <- BiclustSet@ColumnMembership[x, ]
iGroupRows <- BiclustSet@GenesMembership[, x]
superBiclusterSamples <- as.logical(colSums(iGroupColumns) == nrow(iGroupColumns))
superBiclusterGenes <- as.logical(rowSums(iGroupRows) == ncol(iGroupRows))
plotProfilesAcrossAllSamples(x = data,superBiclusterGenes, superBiclusterSamples)
}
plotProfilesAcrossAllSamples <- function(x, coreBiclusterGenes, coreBiclusterSamples){
namesS <- colnames(x)
grp <- rep(1, length(namesS))
grp[coreBiclusterSamples] <- 2
matplot(y = t(x[coreBiclusterGenes , order(grp, decreasing=TRUE) ]), type = "n", xlab="",ylab="Expression", axes=FALSE,
pch = rep(1, ncol(x)))
matlines(y = t(x[coreBiclusterGenes , order(grp, decreasing=TRUE) ]), type = "l",
lty = rep(1, nrow(x)) , col = "black", lwd = 1, pch = 1)
matlines(y = t(x[coreBiclusterGenes ,(grp==2) ]), type = "l",
lty = rep(1, nrow(x)) , col = "red", lwd = 1, pch = 1)
# axis(1, 1:length(namesS), namesS[order(grp, decreasing = TRUE)], cex = 1, las=2)
axis(2)
box()
}
plotProfilesWithinBicluster <- function(x, main = "", sampleNames, geneNames = NULL){
if (!length(sampleNames) == ncol(x))
stop("'sampleNames' should be of length equal to the number of columns of 'x'")
matplot(y = t(x), type = "n", xlab = "", ylab = "Expression", axes=FALSE,
pch = rep(1, ncol(x)))
title(main = main)
axis(1, 1: length(sampleNames), sampleNames, cex=1, par(las=2))
axis(2)
box() #- to make it look "as usual"
if (length(geneNames)){
if (!length(geneNames) == nrow(x))
stop("'geneNames' should be of length equal to the number of rows of 'x'")
matlines(y=t(x), type = "l", lty=rep(1,5000) , col=1:length(geneNames),lwd = 1, pch = NULL)
legend(x="top", legend= geneNames , col = 1:length(geneNames),
border="none",ncol=3, lty=1, lwd=1,merge = TRUE)
} else matlines(y=t(x), type = "l", lty=rep(1,5000) , col=rep(1,5000),lwd = 1, pch = rep(1,5000))
}
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