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#'@title
#'Method to obtain the Volcano Plot.
#'@description
#'\code{plotVolcano} returns a generalized volcano plot where the x-axis
#'represents the difference between isoform's relative expression in the
#'contrasted conditions. Isoforms are colored according to the differential
#'splicing status of the gene where they come from.
#'@param myNBRes NBSpliceRes class object.
#'@param adjusted Logical indicating if adjusted p values should be used.
#'@param p.value Numeric value between 0 and 1 giving the required family-wise
#'error rate or false discovery rate.
#'
#'@return A ggplot object.
#'
#'@include NBSpliceRes-plotRatiosDisp.R
#'@exportMethod plotVolcano
#'@docType methods
#'@name plotVolcano
#'@rdname NBSpliceRes-plotVolcano
#'@import ggplot2
#'@import reshape2
#'@importFrom reshape2 melt
#'@importFrom ggplot2 ggplot
#'@importFrom ggplot2 geom_point
#'@aliases plotVolcano-methods
#'@seealso \code{\link{NBSpliceRes}}
#'@note see full example in \code{\link{NBSpliceRes-class}}
#'@family NBSpliceRes
#'@author Gabriela A. Merino \email{merino.gabriela33@@gmail.com} and Elmer A.
#'Fernandez \email{efernandez@bdmg.com.ar}
#'@examples
#'data(myDSResults, package="NBSplice")
#'
#'g<-plotVolcano(myDSResults)
#'if(interactive()){
#'g
#'}
setGeneric(name="plotVolcano", def=function(myNBRes, adjusted=TRUE,
p.value=0.05){
standardGeneric("plotVolcano")
})
#'@name plotVolcano
#'@rdname NBSpliceRes-plotVolcano
#'@aliases plotVolcano,NBSpliceRes-method
#'@inheritParams plotVolcano
setMethod(f="plotVolcano", signature="NBSpliceRes", definition=function(
myNBRes, adjusted=TRUE, p.value=0.05){
DSDF<-results(myNBRes)
DSDF<-DSDF[!is.na(DSDF[, "pval"]),]
condVars<-colnames(DSDF)[grep("ratio", colnames(DSDF))]
colnames(DSDF)[grep("ratio", colnames(DSDF))]<-c("x", "y")
DSDF$ratDif<-DSDF[,"y"]-DSDF[,"x"]
ratDif<-FDR<-DiffSpl<-pval<-NULL
if(adjusted){
DSDF[,"DiffSpl"]<-DSDF[,"geneFDR"] < p.value & !is.na( DSDF[,
"geneFDR"])
g<-ggplot(DSDF, aes(x=ratDif, y=-log10(FDR), color=DiffSpl))+
geom_point()+labs(x=paste(condVars[2], "-", condVars[1], sep=""))
}else{
DSDF[,"DiffSpl"]<-DSDF[,"genePval"] < p.value & !is.na( DSDF[,
"genePval"])
g<-ggplot(DSDF, aes(x=ratDif, y=-log10(pval), color=DiffSpl))+
geom_point()+labs(x=paste(condVars[2], "-", condVars[1], sep=""))
}
g<-g+theme(panel.background=element_rect(fill="white", color="black"),
legend.key=element_rect( fill="white", color="white"),
panel.grid.major=element_line(color="lightgoldenrod3"),
panel.grid.minor=element_line(color="tomato", linetype = "dashed"),
legend.text = element_text(size = 12),legend.title = element_text(
size = 14, face = "bold"), axis.text=element_text(size=12),
plot.title=element_text(size=14, hjust=0.5), axis.title=element_text(
size=14))+scale_color_manual(values=c("TRUE"="green", "FALSE"="red"))
return(g)
})
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