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# Scree Plot of Kullback Leibler Distance Ratios
# Author: Fan Gao
# Created 25 Seq 2015. Last modified 10 Oct 2016.
timeSeq.screeplot <- function(timeSeq.obj,type=c("barplot","lines")) {
graphics.off()
obj.sorted <- timeSeq.obj$sorted
obj.sorted <- obj.sorted$npde.list
gene.length <- sum(!is.na(obj.sorted[,2]))
gene.index <- !(is.na(obj.sorted[,2]))
if(timeSeq.obj$pvalue){
if (type=="barplot") {
obj.sorted$genenames <- factor(obj.sorted$genenames,
levels=unique(as.character(obj.sorted$genenames)))
barchart(pvalues~genenames,data=obj.sorted,
main="P-values of Genes",xlab="Genes",ylab="P-values",
col = "aliceblue")
} else if (type=="lines") {
plot(x=1:gene.length,y=obj.sorted$pvalues[gene.index],
type="b",pch=21,col="red",xaxt="n",lty = 2,
main="P-values of Genes",xlab="Genes",ylab = "P-values")
axis(1,1:gene.length,obj.sorted$genenames[gene.index],col.axis="blue")
} else {
cat("The type of plot must be bar plot or line graph.\n")
return(cat("ERROR!"))
}
} else {
if (type=="barplot") {
obj.sorted$genenames <- factor(obj.sorted$genenames,
levels=unique(as.character(obj.sorted$genenames)))
barchart(ratios~genenames,data=obj.sorted,
main="Ratios of Genes",xlab="Genes",ylab="Ratios",
col = "aliceblue")
} else if (type=="lines") {
plot(x=1:gene.length,y=obj.sorted$ratios[gene.index],
type="b",pch=21,col="red",xaxt="n",lty = 2,
main="Ratios of Genes",xlab="Genes",ylab = "Ratios")
axis(1,1:gene.length,obj.sorted$genenames[gene.index],col.axis="blue")
} else {
cat("The type of plot must be bar plot or line graph.\n")
return(cat("ERROR!"))
}
}
}
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