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###############################################################################
# Project: biclustRank
## Nolen Joy Perualila (nolenjoy.perualila@uhasselt.be)
###############################################################################
#' @title cdf of similarity scores
#' @param data = data used in biclustering (e.g., expression matrix)
#' @param biclustRes = biclustering output
#' @param p = number of biclusters
#' @param simMat <- similarity matrix from getSimilarity
#' @return a list containing similarity matrix per bicluster
#' @author Nolen Joy Perualila (nolenjoy.perualila@uhasselt.be)
plotFabia<- function(resFabia,bicRes, bcNum, plot=c(1,2)){
if(plot==1){
par(mar=c(2,3.5,2,2))
plot(resFabia@L[,bcNum], type="p",
# main=paste("FABIA factor loadings",bcNum, sep=""),
# xlab="gene index",
ylab=" ",
pch=21,
bg="grey",
col="grey",
cex=2,
# ylim = c(-0.4, 0.1),
axes=FALSE
)
gComb <- unlist(sapply(bicRes[paste("BC",bcNum,sep="")], "[[", 2) )
labelGpos <- match(gComb,rownames(resFabia@L))
text(labelGpos,resFabia@L[gComb,bcNum], gComb,
pos=1,
cex=0.8,
col=bcNum)
points(labelGpos, resFabia@L[gComb,bcNum],
pch=21, bg="grey", cex=2, col="black"
)
#points(labelgClust, fabRes@L[labelgClust,bcNum],
#
# pch=21, bg="grey"
#)
axis(2)
mtext(" Loadings", side = 2, line=2, las=0,
cex=1.5)
mtext("Gene index", side = 1, line=0.5, las=0,
cex=1.5)
#legend("topright",c("Fabia","HC"),
# text.col = c("blue","black"), pch=c(24,21), pt.bg=c("grey",'grey'))
box()
}
else if(plot==2){
par(mar=c(2,3.5,2,2))
plot(resFabia@Z[bcNum,],
ylab=" ",
pch=21,
cex=2,
col="grey",bg="grey",
axes=FALSE)
cFabia <- unlist(sapply(bicRes[paste("BC",bcNum,sep="")], "[[", 1) )
#cFabia <- bicList[[bcNum]][[1]]
labelCpos <- match(cFabia,names(resFabia@Z[bcNum,]))
points(labelCpos, as.vector(resFabia@Z[bcNum,cFabia]),
pch=21, bg="grey", col=bcNum, cex=2
)
text(labelCpos, as.vector(resFabia@Z[bcNum,cFabia]),
cFabia,
cex=0.8,
col=bcNum, pos=3
)
axis(2)
mtext("FABIA Scores", side = 2, line=2, las=0,
cex=1.5)
mtext("Compound index", side = 1, line=0.5, las=0,
cex=1.5)
box()
}
else{stop("plot should be either 1=loadings or 2=scores but not both.")
}
}
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