@@ -62,7 +62,7 @@ plotManyRegions <- function(BSseq, regions = NULL, extend = 0, main = "", addReg

 .bsHighlightRegions <- function(regions, gr, ylim, regionCol, highlightMain) {

     if(is.data.frame(regions))

-        regions <- data.frame2Granges(regions)

+        regions <- data.frame2GRanges(regions)

     if(highlightMain)

         regions <- c(regions, gr)

     if(is.null(regions)) return(NULL)

@@ -77,30 +77,57 @@ plotManyRegions <- function(BSseq, regions = NULL, extend = 0, main = "", addReg

 .bsGetCol <- function(object, col, lty, lwd) {

     ## Assumes that object has pData and sampleNames methods

-    if(is.null(col) & "col" %in% names(pData(object)))

+    if(is.null(col) && "col" %in% names(pData(object)))

         col <- pData(object)[["col"]]

     else

-        col <- rep("black", ncol(pData(object)))

+        col <- rep("black", nrow(pData(object)))

     if(is.null(names(col)))

         names(col) <- sampleNames(object)

-    if(is.null(lty) & "lty" %in% names(pData(object)))

+    if(is.null(lty) && "lty" %in% names(pData(object)))

         lty <- pData(object)[["lty"]]

     else

-        lty <- rep(1, ncol(pData(object)))

+        lty <- rep(1, nrow(pData(object)))

     if(is.null(names(lty)))

         names(lty) <- sampleNames(object)

-    if(is.null(lwd) & "lwd" %in% names(pData(object)))

+    if(is.null(lwd) && "lwd" %in% names(pData(object)))

         lwd <- pData(object)[["lwd"]]

     else

-        lwd <- rep(1, ncol(object))

+        lwd <- rep(1, nrow(pData(object)))

     if(is.null(names(lwd)))

         names(lwd) <- sampleNames(object)

     return(list(col = col, lty = lty, lwd = lwd))

 }

+.bsPlotTitle <- function(gr, extend, main, mainWithWidth) {

+    if(is.data.frame(gr))

+        gr <- data.frame2GRanges(gr)

+    if(length(gr) > 1) {

+        warning("plotTitle: gr has more than one element")

+        gr <- gr[1]

+    }

+    plotChr <- as.character(seqnames(gr))

+    plotRange <- c(start(gr), end(gr))

+    regionCoord <- sprintf("%s: %s - %s", plotChr, 

+                           format(plotRange[1], big.mark = ",", scientific = FALSE),

+                           format(plotRange[2], big.mark = ",", scientific = FALSE))

+    if(mainWithWidth) {

+        regionWidth <- sprintf("width = %s, extended = %s", 

+                               format(width(gr) - 2*extend, big.mark = ",", scientific = FALSE),

+                               format(extend, big.mark = ",", scientific = FALSE))

+        regionCoord <- sprintf("%s (%s)", regionCoord, regionWidth)

+    }

+    if(main != "") {

+        main <- sprintf("%s\n%s", main, regionCoord)

+    } else {

+        main <- regionCoord

+    }

+    main

+}

+

+

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

                             addTicks, addPoints, pointsMinCov, highlightMain) {

     if(is.data.frame(region))

@@ -128,8 +155,7 @@ plotManyRegions <- function(BSseq, regions = NULL, extend = 0, main = "", addReg

     smoothPs <- getMeth(BSseq, type = "smooth")

     rawPs <- getMeth(BSseq, type = "raw")

     coverage <- getCoverage(BSseq)

-    plotRange

-    

+        

     ## get col, lwd, lty

     colEtc <- bsseq:::.bsGetCol(object = BSseq, col = col, lty = lty, lwd = lwd)

@@ -140,7 +166,7 @@ plotManyRegions <- function(BSseq, regions = NULL, extend = 0, main = "", addReg

     if(addTicks)

         rug(positions)

-    .bsHighlightRegions(regions = regions, gr = gr, ylim = c(0,1),

+    .bsHighlightRegions(regions = addRegions, gr = gr, ylim = c(0,1),

                         regionCol = regionCol, highlightMain = highlightMain)

     if(addPoints) {

@@ -164,7 +190,7 @@ plotManyRegions <- function(BSseq, regions = NULL, extend = 0, main = "", addReg

 }

-newPlotRegion <- function(BSseq, region = NULL, extend = 0, main = "", addRegions = NULL, annoTrack = NULL,

+plotRegion <- function(BSseq, region = NULL, extend = 0, main = "", addRegions = NULL, annoTrack = NULL,

                           col = NULL, lty = NULL, lwd = NULL, BSseqTstat = NULL, mainWithWidth = TRUE,

                           regionCol = alpha("red", 0.1), addTicks = TRUE, addPoints = FALSE,

                           pointsMinCov = 5, highlightMain = FALSE) {

@@ -200,198 +226,14 @@ newPlotRegion <- function(BSseq, region = NULL, extend = 0, main = "", addRegion

         bsseq:::plotAnnoTrack(gr, annoTrack)

     if(!is.null(main)) {

-        main <- makePlotTitle(gr = gr, extend = extend, main = main, mainWithWidth = mainWithWidth)

-        mtext(side = 3, text = main, outer = TRUE, cex = 1)

-    }

-    return(invisible(NULL))

-}

-

-    

-

-plotRegion <- function(BSseq, region = NULL, extend = 0, main = "", addRegions = NULL, annoTrack = NULL,

-                       col = NULL, lty = NULL, lwd = NULL, BSseqTstat = NULL, mainWithWidth = TRUE,

-                       regionCol = alpha("red", 0.1), addTicks = TRUE, addPoints = FALSE,

-                       pointsMinCov = 5, highlightMain = FALSE) {

-    makeTitle <- function(gr, extend, main, mainWithWidth) {

-        if(length(gr) > 1) {

-            warning("plotTitle: gr has more than one element")

-            gr <- gr[1]

-        }

-        plotChr <- as.character(seqnames(gr))

-        plotRange <- c(start(gr), end(gr))

-        regionCoord <- sprintf("%s: %s - %s", plotChr, 

-                               format(plotRange[1], big.mark = ",", scientific = FALSE),

-                               format(plotRange[2], big.mark = ",", scientific = FALSE))

-        if(mainWithWidth) {

-            regionWidth <- sprintf("width = %s, extended = %s", 

-                                   format(width(gr) - 2*extend, big.mark = ",", scientific = FALSE),

-                                   format(extend, big.mark = ",", scientific = FALSE))

-            regionCoord <- sprintf("%s (%s)", regionCoord, regionWidth)

-        }

-        if(main != "") {

-            main <- sprintf("%s\n%s", main, regionCoord)

-        } else {

-            main <- regionCoord

-        }

-        main

-    }

-    plotRects <- function(ylim) {

-        if(!is.null(addRegions))

-            rect(xleft = addRegions$start, xright = addRegions$end, ybottom = ylim[1],

-                 ytop = ylim[2], col = regionCol, border = NA)

-    }

-    restrictRegions <- function(regions, plotRange, plotChr) {

-        if(is.null(regions)) return(NULL)

-        regions <- regions[regions$chr == plotChr &

-                           ((regions$start >= plotRange[1] &

-                             regions$start <= plotRange[2]) |

-                           (regions$end >= plotRange[1] &

-                            regions$end <= plotRange[2])),, drop = FALSE]

-        if(nrow(regions) == 0)

-            regions <- NULL

-        regions

-    }

-    plotLines <- function(x, y, lty, col, lwd, plotRange) {

-        if(sum(!is.na(y)) <= 1)

-            return(NULL)

-        xx <- seq(from = plotRange[1], to = plotRange[2], length.out = 2000)

-        yy <- approxfun(x, y)(xx)

-        lines(xx, yy, col = col, lty = lty, lwd = lwd)

-    }

-    plotPoints <- function(x, y, z, col) {

-        points(x[z>pointsMinCov], y[z>pointsMinCov], col = col, pch = 16, cex = 0.5)

-        ## sample, label = "", col) {

-        ## plot(positions[1], 0.5, type = "n", xaxt = "n", yaxt = "n",

-        ##      ylim = c(0,1), xlim = plotRange, xlab = "", ylab = "")

-        ## plotRects(c(0,1))

-        ## rawp <- getP(BSseq, sample = sample, type = "raw", addPositions = TRUE, addConfint = TRUE)

-        ## cols <- rep(alpha("black", 0.5), nrow(rawp))

-        ## segments(x0 = rawp$pos, y0 = rawp$lower, y1 = rawp$upper, col = cols)

-        ## points(positions, rawp$p, col = cols)

-        ## if(nrow(BSseq$coef) > 0) {

-        ##     fitp <- getP(BSseq, sample = sample, type = "fit", addPosition = TRUE, addConfint = FALSE) 

-        ##     lines(fitp$pos, fitp$p, col = col,, lty = 1)

-        ##     ## lines(fitp$pos, fitp$lower, col = col, lty = 2)

-        ##     ## lines(fitp$pos, fitp$upper, col = col, lty = 2)

-        ##     text(plotRange[1], 0.1, labels = label)

-        ## }

-    }

-    

-    ## First we create a basic GRanges which will be the plotting region

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

-        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))))

-    }

-    origWidth <- width(gr)

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

-    plotRange <- c(start(gr), end(gr))

-    plotChr <- as.character(seqnames(gr))[1]

-    BSseq <- subsetByOverlaps(BSseq, gr)

-    if(!is.null(BSseqTstat))

-        BSseqTstat <- subsetByOverlaps(BSseqTstat, gr)

-    positions <- start(BSseq)

-    if(length(positions) == 0) {

-        warning("No overlap between BSseq data and region")

-        return(NULL)

-    }

-        

-    ## Now for some plotting

-    opar <- par(mar = c(0,4.1,0,0), oma = c(5,0,4,2), mfrow = c(1,1))

-    on.exit(par(opar))

-    if(is.null(BSseqTstat))

-        layout(matrix(1:2, ncol = 1), heights = c(2,1))

-    else

-        layout(matrix(1:3, ncol = 1), heights = c(2,2,1))

-       

-    sampleNames <- sampleNames(BSseq)

-    names(sampleNames) <- sampleNames

-    plot(positions[1], 0.5, type = "n", xaxt = "n", yaxt = "n",

-         ylim = c(0,1), xlim = plotRange, xlab = "", ylab = "Methylation")

-    axis(side = 2, at = c(0.2, 0.5, 0.8))

-    if(addTicks)

-        rug(positions)

-

-    addRegions <- restrictRegions(addRegions, plotRange = plotRange, plotChr = plotChr)

-    if(highlightMain)

-        addRegions <- rbind(region[, c("chr", "start", "end")],

-                            addRegions[, c("chr", "start", "end")])

-    if(!is.null(addRegions))

-        plotRects(c(0,1))

-

-    smoothPs <- getMeth(BSseq, type = "smooth")

-    rawPs <- getMeth(BSseq, type = "raw")

-    coverage <- getCoverage(BSseq)

-    

-    if(is.null(col) & "col" %in% names(pData(BSseq)))

-        col <- pData(BSseq)[["col"]]

-    else

-        col <- rep("black", ncol(BSseq))

-    if(is.null(names(col)))

-        names(col) <- sampleNames(BSseq)

-    if(is.null(lty) & "lty" %in% names(pData(BSseq)))

-        lty <- pData(BSseq)[["lty"]]

-    else

-        lty <- rep(1, ncol(BSseq))

-    if(is.null(names(lty)))

-        names(lty) <- sampleNames(BSseq)

-    if(is.null(lwd) & "lwd" %in% names(pData(BSseq)))

-        lwd <- pData(BSseq)[["lwd"]]

-    else

-        lwd <- rep(1, ncol(BSseq))

-    if(is.null(names(lwd)))

-        names(lwd) <- sampleNames(BSseq)

-

-    if(addPoints) {

-        sapply(sampleNames(BSseq), function(samp) {

-            abline(v = positions[rawPs[, samp] > 0.1], col = "grey80", lty = 1)

-        })

-    }

-

-    sapply(sampleNames(BSseq), function(samp) {

-        plotLines(positions, smoothPs[, samp], col = col[samp],

-                  lty = lty[samp], lwd = lwd[samp], plotRange = plotRange)

-    })

-

-    if(addPoints) {

-        sapply(sampleNames(BSseq), function(samp) {

-            plotPoints(positions, rawPs[, samp], coverage[, samp], col = col[samp])

-        })

-    }

-    

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

-        plot(positions[1], 0.5, type = "n", xaxt = "n", yaxt = "n",

-             ylim = c(-8,8), xlim = plotRange, xlab = "", ylab = "t-stat")

-        axis(side = 2, at = c(-5,0,5))

-        abline(h = 0, col = "grey60")

-        plotLines(start(BSseqTstat), BSseqTstat@stats[, "tstat"],

-                  lty = 1, plotRange = plotRange, col = "red", lwd = 1)

-        plotLines(start(BSseqTstat), BSseqTstat@stats[, "tstat.corrected"],

-                  lty = 2, plotRange = plotRange, col = "red", lwd = 1)

-        plotLines(start(BSseqTstat), 100*BSseqTstat@stats[, "tstat.sd"],

-                  lty = 2, plotRange = plotRange, col = "blue", lwd = 1)

-    }

-    

-

-    if(!is.null(annoTrack))

-        bsseq:::plotAnnoTrack(gr, annoTrack)

-

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

-        main <- makePlotTitle(gr = gr, extend = extend, main = main, mainWithWidth = mainWithWidth)

+        main <- bsseq:::.bsPlotTitle(gr = region, extend = extend, main = main,

+                                     mainWithWidth = mainWithWidth)

         mtext(side = 3, text = main, outer = TRUE, cex = 1)

     }

     return(invisible(NULL))

 }

-

-

+ 

 ##     plotP <- function(sample, label = "", col) {

 ##         plot(positions[1], 0.5, type = "n", xaxt = "n", yaxt = "n",

 ##              ylim = c(0,1), xlim = plotRange, xlab = "", ylab = "")