@@ -425,7 +425,9 @@ plotBoxplot <- function(model) {

 #' @param chr,start,end Chromosome, start and end coordinates for the plot.

 #' @param style One of \code{c('peaks', 'density')}.

 #' @param peakHeight Height of the peak track relative to the count track.

-#' @return A \code{\link[ggplot2:ggplot]{ggplot}} object.

+#' @param peakColor Color for the peak track.

+#' @param same.yaxis Whether or not the plots for the same mark have the same y-axis.

+#' @return A \code{list()} of \code{\link[ggplot2:ggplot]{ggplot}} objects.

 #' @export

 #' @examples

 #'## Get an example uniHMM ##

@@ -448,7 +450,7 @@ plotBoxplot <- function(model) {

 #'plotlist <- plotGenomeBrowser(model, chr='chr12', start=1, end=1e6, style='peaks',

 #'                  peakHeight=0.1)

 #'

-plotGenomeBrowser <- function(model, chr, start, end, style='peaks', peakHeight=0.2) {

+plotGenomeBrowser <- function(model, chr, start, end, style='peaks', peakHeight=0.2, peakColor='blue', same.yaxis=TRUE) {

     model <- loadHmmsFromFiles(model, check.class = c('uniHMM', 'multiHMM', 'combinedMultiHMM'))[[1]]

@@ -478,15 +480,20 @@ plotGenomeBrowser <- function(model, chr, start, end, style='peaks', peakHeight=

     ggplts <- list()

     for (i1 in 1:nrow(model$info)) {

-        ymax.counts <- round(maxcounts.permark[[as.character(model$info$mark[i1])]])

         ID <- model$info$ID[i1]

+        

+        if (same.yaxis) {

+            ymax.counts <- round(maxcounts.permark[[as.character(model$info$mark[i1])]])

+        } else {

+            ymax.counts <- round(maxcounts[[as.character(ID)]])

+        }

         if (style == 'peaks') {

             df <- data.frame(position=(start(bins)+end(bins))/2, RPKM=bins$counts.rpkm[,ID]) # plot triangles centered at middle of the bin

             ggplt <- ggplot(df) + geom_area(aes_string(x='position', y='RPKM')) + theme(panel.grid = element_blank(), panel.background = element_blank(), axis.line = element_blank())

         } else if (style == 'density') {

             df <- data.frame(xmin=start(bins), xmax=end(bins), RPKM=bins$counts.rpkm[,ID])

-            ggplt <- ggplot(df) + geom_rect(aes_string(xmin='xmin', xmax='xmax', ymin=0, ymax.counts=4, alpha='RPKM')) + theme(panel.grid = element_blank(), panel.background = element_blank(), axis.text.y = element_blank(), axis.ticks.y = element_blank(), axis.line = element_blank(), axis.title.y = element_blank())

+            ggplt <- ggplot(df) + geom_rect(aes_string(xmin='xmin', xmax='xmax', ymin=0, ymax=4, alpha='RPKM')) + theme(panel.grid = element_blank(), panel.background = element_blank(), axis.text.y = element_blank(), axis.ticks.y = element_blank(), axis.line = element_blank(), axis.title.y = element_blank())

             ggplt <- ggplt + xlab('position')

         } else {

             stop("Unknown value '", style, "' for parameter 'style'. Must be one of c('peaks', 'density').")

@@ -496,10 +503,11 @@ plotGenomeBrowser <- function(model, chr, start, end, style='peaks', peakHeight=

         peaks <- subsetByOverlaps(peaklist[[ID]], ranges2plot)

         if (length(peaks) > 0) {

             df <- data.frame(start=start(peaks), end=end(peaks), ymin=-peakHeight*ymax.counts, ymax=0.1*(-peakHeight*ymax.counts))

-            ggplt <- ggplt + geom_rect(data=df, mapping=aes_string(xmin='start', xmax='end', ymin='ymin', ymax='ymax'), col='blue', fill='blue')

+            ggplt <- ggplt + geom_rect(data=df, mapping=aes_string(xmin='start', xmax='end', ymin='ymin', ymax='ymax'), col=peakColor, fill=peakColor)

         }

-        ggplt <- ggplt + scale_y_continuous(breaks=c(0, ymax.counts)) + coord_cartesian(xlim=c(start, end), ylim=c(-peakHeight*ymax.counts,ymax.counts))

+        ggplt <- ggplt + scale_y_continuous(breaks=c(0, ymax.counts))

+        ggplt <- ggplt + coord_cartesian(xlim=c(start, end), ylim=c(-peakHeight*ymax.counts,ymax.counts))

         ggplt <- ggplt + ggtitle(ID)

         ggplts[[ID]] <- ggplt

     }

@@ -99,6 +99,7 @@ unis2pseudomulti <- function(hmms) {

     rownames(result$info) <- NULL

     result$bins <- bins

     ## Segmentation

+        ptm <- startTimedMessage("Segmentation ...")

         df <- as.data.frame(result$bins)

         ind.readcols <- grep('^counts', names(df))

         ind.widthcol <- grep('width', names(df))

@@ -107,6 +108,7 @@ unis2pseudomulti <- function(hmms) {

         red.gr <- GRanges(seqnames=red.df[,1], ranges=IRanges(start=red.df[,2], end=red.df[,3]), strand=red.df[,4], state=red.df[,'state'], combination=red.df[,'combination'])

         result$segments <- red.gr

         seqlengths(result$segments) <- seqlengths(result$bins)[seqlevels(result$segments)]

+        stopTimedMessage(ptm)

     ## Parameters

         result$mapping <- mapping

         # Weights

@@ -125,6 +127,10 @@ unis2pseudomulti <- function(hmms) {

     ## Add class

         class(result) <- class.multivariate.hmm

+    ## Get the peaks ##

+        result$peaks <- lapply(hmms, '[[', 'peaks')

+        names(result$peaks) <- result$info$ID

+        

     return(result)

 }

@@ -68,7 +68,8 @@ plotGenomeBrowser2 <- function(counts, peaklist=NULL, chr, start, end, countcol=

 }

 Plot a genome browser view}

 \usage{

-plotGenomeBrowser(model, chr, start, end, style = "peaks", peakHeight = 0.2)

+plotGenomeBrowser(model, chr, start, end, style = "peaks", peakHeight = 0.2,

+  peakColor = "blue", same.yaxis = TRUE)

 }

 \arguments{

 \item{model}{A \code{\link{uniHMM}}, \code{\link{multiHMM}} or \code{\link{combinedMultiHMM}} object or file that contains such an object.}

@@ -78,9 +79,13 @@ plotGenomeBrowser(model, chr, start, end, style = "peaks", peakHeight = 0.2)

 \item{style}{One of \code{c('peaks', 'density')}.}

 \item{peakHeight}{Height of the peak track relative to the count track.}

+

+\item{peakColor}{Color for the peak track.}

+

+\item{same.yaxis}{Whether or not the plots for the same mark have the same y-axis.}

 }

 \value{

-A \code{\link[ggplot2:ggplot]{ggplot}} object.

+A \code{list()} of \code{\link[ggplot2:ggplot]{ggplot}} objects.

 }

 \description{

 Plot a simple genome browser view of \code{\link{chromstaR-objects}}. This is useful for scripted genome browser snapshots.