@@ -127,25 +127,27 @@ plotManyRegions <- function(BSseq, regions = NULL, extend = 0, main = "", addReg

     main

 }

-

-.plotSmoothData <- function(BSseq, region, extend, addRegions, col, lty, lwd, regionCol,

-                            addTicks, addPoints, pointsMinCov, highlightMain) {

-    if(is.data.frame(region))

-        region <- data.frame2GRanges(region)

-

-    if(!is.null(region)) {

+.bsGetGr <- function(object, region, extend) {

+    if(is.null(region)) {

+        gr <- GRanges(seqnames = seqnames(object)[1],

+                      ranges = IRanges(start = min(start(object)),

+                      end = max(start(object))))

+    } else {

         if(is(region, "data.frame"))

             gr <- data.frame2GRanges(region, keepColumns = FALSE)

         else

             gr <- region

         if(!is(gr, "GRanges") || length(gr) != 1)

             stop("'region' needs to be either a 'data.frame' (with a single row) or a 'GRanges' (with a single element)")

-    } else {

-        gr <- GRanges(seqnames = seqnames(BSseq)[1],

-                      ranges = IRanges(start = min(start(BSseq)),

-                      end = max(start(BSseq))))

+        gr <- resize(gr, width = 2*extend + width(gr), fix = "center")

     }

-    gr <- resize(gr, width = 2*extend + width(gr), fix = "center")

+    gr

+}

+

+

+.plotSmoothData <- function(BSseq, region, extend, addRegions, col, lty, lwd, regionCol,

+                            addTicks, addPoints, pointsMinCov, highlightMain) {

+    gr <- .bsGetGr(Bsseq, region, extend)

     BSseq <- subsetByOverlaps(BSseq, gr)

     ## Extract basic information

@@ -206,7 +208,8 @@ plotRegion <- function(BSseq, region = NULL, extend = 0, main = "", addRegions =

                             col = col, lty = lty, lwd = lwd, regionCol = regionCol,

                             addTicks = addTicks, addPoints = addPoints,

                             pointsMinCov = pointsMinCov, highlightMain = highlightMain)

-

+    gr <- .bsGetGr(BSseq, region, extend)

+    

     if(!is.null(BSseqTstat)) {

         if(!is.null(BSseqTstat))

             BSseqTstat <- subsetByOverlaps(BSseqTstat, gr)