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setGeneric("syntenicDotplot",
function(x, firstSeqlengths=NULL, secondSeqlengths=NULL,
firstChrs=NULL, secondChrs=NULL,
col=c("blue", "red"), type=c("line", "dot"))
standardGeneric("syntenicDotplot"))
setMethod("syntenicDotplot", signature=(x="GRangePairs"),
function(x, firstSeqlengths=NULL, secondSeqlengths=NULL,
firstChrs=NULL, secondChrs=NULL,
col=c("blue", "red"), type=c("line", "dot")){
syntenicPlotGRangePairs(x, firstSeqlengths=firstSeqlengths,
secondSeqlengths=secondSeqlengths,
firstChrs=firstChrs,
secondChrs=secondChrs,
col=col, type=type)
})
syntenicPlotGRangePairs <- function(x, firstSeqlengths=NULL,
secondSeqlengths=NULL,
firstChrs=NULL, secondChrs=NULL,
col=c("blue", "red"),
type=c("line", "dot")){
type <- match.arg(type)
if(is.null(firstSeqlengths)){
targetSeqlengths <- seqlengths(first(x))
if(any(is.na(targetSeqlengths))){
stop("When firstSeqlengths is NULL, the seqlengths must exist in x!")
}
}else{
targetSeqlengths <- firstSeqlengths
}
if(is.null(secondSeqlengths)){
querySeqlengths <- seqlengths(second(x))
if(any(is.na(querySeqlengths))){
stop("When secondSeqlengths is NULL, the seqlengths must exist in x!")
}
}else{
querySeqlengths <- secondSeqlengths
}
if(!is.null(firstChrs)){
x <- x[seqnames(first(x)) %in% firstChrs]
targetSeqlengths <- targetSeqlengths[firstChrs]
}
if(!is.null(secondChrs)){
x <- x[seqnames(second(x)) %in% secondChrs]
querySeqlengths <- querySeqlengths[secondChrs]
}
target <- first(x)
query <- second(x)
## If we want to put all the segments of syntent in one plot
## We need to shift the coordiantes from second chromosomes in seqlengths
shiftCoordinatesTarget <- c(0, cumsum(as.numeric(targetSeqlengths))[-length(targetSeqlengths)])
names(shiftCoordinatesTarget) <- names(targetSeqlengths)
shiftCoordinatesQuery <- c(0, cumsum(as.numeric(querySeqlengths))[-length(querySeqlengths)])
names(shiftCoordinatesQuery) <- names(querySeqlengths)
startTarget <- start(target) +
shiftCoordinatesTarget[as.character(seqnames(target))]
endTarget <- end(target) +
shiftCoordinatesTarget[as.character(seqnames(target))]
startQuery <- start(query) +
shiftCoordinatesQuery[as.character(seqnames(query))]
endQuery <- end(query) +
shiftCoordinatesQuery[as.character(seqnames(query))]
combinedStrands <- rep("+", length(target))
combinedStrands[xor(as.character(strand(target))=="+",
as.character(strand(query))=="+")] <- "-"
toPlot <- data.frame(x=startTarget, xEnd=endTarget,
y=startQuery, yEnd=endQuery,
strand=factor(combinedStrands, levels=c("+", "-")))
if(type == "line"){
p <- ggplot(data=toPlot, aes_string(x="x",y="y", xend="xEnd", yend="yEnd")) +
geom_segment(aes(colour=strand)) + theme_bw() +
scale_colour_manual(values=col) +
xlab("First") + ylab("Second") + ggtitle("Syntenic dotplot") +
scale_x_continuous(breaks=c(0,
cumsum(as.numeric(targetSeqlengths))),
limits=c(0, sum(as.numeric(targetSeqlengths))),
labels=c("start", names(targetSeqlengths))) +
scale_y_continuous(breaks=c(0,
cumsum(as.numeric(querySeqlengths))),
limits=c(0, sum(as.numeric(querySeqlengths))),
labels=c("start", names(querySeqlengths)))
}else if(type == "dot"){
p <- ggplot(data=toPlot, aes_string(x="x",y="y")) +
geom_point(aes(colour=strand), size=0.5) + theme_bw() +
scale_colour_manual(values=col) +
xlab("First") + ylab("Second") + ggtitle("Syntenic dotplot") +
scale_x_continuous(breaks=c(0,
cumsum(as.numeric(targetSeqlengths))),
limits=c(0, sum(as.numeric(targetSeqlengths))),
labels=c("start", names(targetSeqlengths))) +
scale_y_continuous(breaks=c(0,
cumsum(as.numeric(querySeqlengths))),
limits=c(0, sum(as.numeric(querySeqlengths))),
labels=c("start", names(querySeqlengths)))
}
p
}
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