@@ -1,6 +1,6 @@

 Package: SplicingGraphs

 Title: Tools for creating splicing graphs from annotations and RNA-Seq data

-Version: 0.98.3

+Version: 0.98.4

 Author: D. Bindreither, M. Carlson, M. Morgan, H. Pages

 License: Artistic-2.0

 Description: This package allows the user to create and manipulate splicing

@@ -62,8 +62,7 @@ export(

     toy_genes_gff,

     toy_reads_sam,

     toy_reads_bam,

-    toy_overlaps,

-    plotToyReads

+    toy_overlaps

 )

@@ -2,32 +2,67 @@

 ### "plotTranscripts" methods

 ### -------------------------------------------------------------------------

+.plotTranscripts.GRangesList <- function(x, reads=NULL, from=NULL, to=NULL)

+{

+    ## Compute the genomic range of the transcripts.

+    unlisted_x <- unlist(x, use.names=FALSE)

+    strand(unlisted_x) <- "*"

+    tx_range <- range(unlisted_x)

+    if (length(tx_range) != 1L)

+        stop("cannot plot transcripts that are on different chromosomes")

-setGeneric("plotTranscripts", function(x) standardGeneric("plotTranscripts"))

+    ## Genome axis.

+    tracks <- list(Gviz::GenomeAxisTrack())

-setMethod("plotTranscripts", "GRangesList",

-    function(x)

-    {

-        track_names <- mcols(x)$tx_id

-        if (is.null(track_names))

-            track_names <- names(x)

-        ### We create 1 track per transcript.

-        tx_tracks <- lapply(seq_along(x),

-                            function(i) {

-                              tx <- x[[i]]

-                              Gviz::AnnotationTrack(tx, name=track_names[i],

-                                                    fill="orange", shape="box")

-                            })

-        ax_track <- Gviz::GenomeAxisTrack()

-        Gviz::plotTracks(c(list(ax_track), tx_tracks))

+    ## Transcript tracks (we create 1 track per transcript).

+    track_names <- mcols(x)$tx_id

+    if (is.null(track_names))

+        track_names <- names(x)

+    tx_tracks <- lapply(seq_along(x),

+                        function(i) {

+                          tx <- x[[i]]

+                          Gviz::AnnotationTrack(tx, name=track_names[i],

+                                                fill="orange", shape="box")

+                        })

+    tracks <- c(tracks, tx_tracks)

+

+    if (!is.null(reads)) {

+        ## Reads track.

+        reads <- grglist(reads, order.as.in.query=TRUE)

+        gr <- unlist(reads)

+        mcols(gr)$group <- names(gr)

+        reads <- relist(unname(gr), reads)

+        name <- if (length(reads) == 1L) names(reads)[1L] else "reads"

+        reads_track <- Gviz::AnnotationTrack(reads, name=name,

+                                             fill="blue", shape="box")

+        tracks <- c(tracks, list(reads_track))

+    }

+

+    if (is.null(from) || is.null(to)) {

+        x_min_start <- start(tx_range)

+        x_max_end <- end(tx_range)

+        margin <- 0.10 * (x_max_end - x_min_start)

+        if (is.null(from))

+            from <- x_min_start - margin

+        if (is.null(to))

+            to <- x_max_end + margin

     }

+

+    Gviz::plotTracks(tracks, from=from, to=to)

+}

+

+setGeneric("plotTranscripts", signature="x",

+    function(x, reads=NULL, from=NULL, to=NULL)

+        standardGeneric("plotTranscripts")

 )

+setMethod("plotTranscripts", "GRangesList", .plotTranscripts.GRangesList)

+

 setMethod("plotTranscripts", "TranscriptDb",

-    function(x)

+    function(x, reads=NULL, from=NULL, to=NULL)

     {

         ex_by_tx <- exonsBy(x, by="tx", use.names=TRUE)

-        plotTranscripts(ex_by_tx)

+        plotTranscripts(ex_by_tx, reads=reads, from=from, to=to)

     }

 )

@@ -36,7 +71,7 @@ setMethod("plotTranscripts", "SplicingGraphs",

     {

         if (length(x) != 1L)

             stop("'x' must be a SplicingGraphs object of length 1")

-        plotTranscripts(x[[1L]])

+        plotTranscripts(x[[1L]], reads=reads, from=from, to=to)

     }

 )

@@ -52,26 +52,3 @@ if (FALSE) {

              from=1, to=9)

 }

-### Uses the Gviz package.

-plotToyReads <- function(gal, txdb, from=NULL, to=NULL)

-{

-    ax_track <- Gviz::GenomeAxisTrack()

-    txdb_track <- Gviz::GeneRegionTrack(txdb, name="genes")

-    grl <- grglist(gal)

-    gr <- unlist(grl)

-    mcols(gr)$group <- names(gr)

-    grl <- relist(unname(gr), grl)

-    name <- if (length(grl) == 1L) names(grl)[1L] else "reads"

-    gal_track <- Gviz::AnnotationTrack(grl, name=name, fill="blue", shape="box")

-    if (is.null(from) || is.null(to)) {

-        gal_min_start <- min(start(gal))

-        gal_max_end <- max(end(gal))

-        margin <- 0.10 * (gal_max_end - gal_min_start)

-        if (is.null(from))

-            from <- gal_min_start - margin

-        if (is.null(to))

-            to <- gal_max_end + margin

-    }

-    Gviz::plotTracks(list(ax_track, gal_track, txdb_track), from=from, to=to)

-}

-

@@ -164,8 +164,8 @@ SplicingGraphs(x, grouping=NULL, min.ntx=2, max.ntx=NA, check.introns=TRUE)

 \seealso{

   \itemize{

-    \item \code{\link[GenomicFeatures]{exonsBy}},

-          \code{\link[GenomicFeatures]{transcriptsBy}}, and the

+    \item The \code{\link[GenomicFeatures]{exonsBy}} and

+          \code{\link[GenomicFeatures]{transcriptsBy}} functions, and the

           \link[GenomicFeatures]{TranscriptDb} class in the GenomicFeatures

           package.

@@ -194,6 +194,9 @@ SplicingGraphs(x, grouping=NULL, min.ntx=2, max.ntx=NA, check.introns=TRUE)

     \item \code{\link{countReads}} for assigning reads to the edges of a

           SplicingGraphs object and summarizing them.

+

+    \item \code{\link{toy_genes_gff}} for details about the toy data included

+          in the SplicingGraphs package.

   }

 }

@@ -261,6 +264,4 @@ sg[["geneD"]]

 ## by transcript. The names on the object are the gene ids:

 ex_by_tx <- unlist(sg)

 ex_by_tx

-

-## See '?plotTranscripts' for how to plot those transcripts.

 }

@@ -56,6 +56,11 @@ countReads(sg)

 \seealso{

   \itemize{

+    \item The \link[GenomicRanges]{GRangesList},

+          \link[GenomicRanges]{GappedAlignments}, and

+          \link[GenomicRanges]{GappedAlignmentPairs} classes

+          in the GenomicRanges package.

+

     \item The \link{SplicingGraphs} class.

     \item \code{\link{sgedgesByGene}} for extracting all the edges and

@@ -18,7 +18,7 @@

 }

 \usage{

-plotTranscripts(x)

+plotTranscripts(x, reads=NULL, from=NULL, to=NULL)

 }

 \arguments{

@@ -28,6 +28,14 @@ plotTranscripts(x)

     \link[GenomicFeatures]{TranscriptDb} object, or a \link{SplicingGraphs}

     object of length 1.

   }

+  \item{reads}{

+    A \link[GenomicRanges]{GappedAlignments} or

+    \link[GenomicRanges]{GappedAlignmentPairs} object containing single-end

+    or paired-end reads.

+  }

+  \item{from, to}{

+    TODO

+  }

 }

 \author{

@@ -39,8 +47,10 @@ plotTranscripts(x)

     \item The \code{\link[Gviz]{plotTracks}} function in the Gviz package

           that \code{plotTranscripts} is based on.

-    \item The \link[GenomicRanges]{GRangesList} class in the GenomicRanges

-          package.

+    \item The \link[GenomicRanges]{GRangesList},

+          \link[GenomicRanges]{GappedAlignments}, and

+          \link[GenomicRanges]{GappedAlignmentPairs} classes

+          in the GenomicRanges package.

     \item The \link[GenomicFeatures]{TranscriptDb} class in the GenomicFeatures

           package.

@@ -49,10 +59,19 @@ plotTranscripts(x)

     \item \code{\link{sgraph}} for extracting a splicing graph as a

           plottable graph-like object.

+

+    \item \code{\link{countReads}} for assigning reads to the edges of a

+          \link{SplicingGraphs} object and summarizing them.

+

+    \item \code{\link{toy_reads_bam}} for details about the toy data included

+          in the SplicingGraphs package.

   }

 }

 \examples{

+## ---------------------------------------------------------------------

+## A. PLOT TRANSCRIPTS

+## ---------------------------------------------------------------------

 example(SplicingGraphs)  # create SplicingGraphs object 'sg'

 sg

@@ -71,4 +90,13 @@ plotTranscripts(sg[["geneD"]])  # requires the Gviz package

 ex_by_tx <- unlist(sg)

 ex_by_tx

 plotTranscripts(ex_by_tx)

+

+## ---------------------------------------------------------------------

+## B. PLOT TRANSCRIPTS AND READS

+## ---------------------------------------------------------------------

+gal <- readGappedAlignments(toy_reads_bam(), use.names=TRUE)

+plotTranscripts(sg[["geneA"]], reads=gal)

+plotTranscripts(ex_by_tx, reads=gal)

+plotTranscripts(ex_by_tx, reads=gal, from=1, to=320)

+plotTranscripts(ex_by_tx, reads=gal[21:26], from=1, to=320)

 }

@@ -5,11 +5,10 @@

 \alias{toy_reads_sam}

 \alias{toy_reads_bam}

 \alias{toy_overlaps}

-\alias{plotToyReads}

 \title{

-  Little helpers for quick access to (and plotting of) the toy data

-  included in the SplicingGraphs package

+  Little helpers for quick access to the toy data included in the

+  SplicingGraphs package

 }

 \description{

@@ -21,22 +20,6 @@ toy_genes_gff()

 toy_reads_sam()

 toy_reads_bam()

 toy_overlaps()

-plotToyReads(gal, txdb, from=NULL, to=NULL)

-}

-

-\arguments{

-  \item{gal}{

-    TODO

-  }

-  \item{txdb}{

-    TODO

-  }

-  \item{from}{

-    TODO

-  }

-  \item{to}{

-    TODO

-  }

 }

 \author{

@@ -44,11 +27,20 @@ plotToyReads(gal, txdb, from=NULL, to=NULL)

 }

 \seealso{

-  The toy data described here is used in the examples of the following

-  man pages:

   \itemize{

-    \item \code{\link{SplicingGraphs}}: Tools for creating and

-          plotting splicing graphs from transcript annotations.

+    \item The \link[GenomicRanges]{GRangesList},

+          \link[GenomicRanges]{GappedAlignments}, and

+          \link[GenomicRanges]{GappedAlignmentPairs} classes

+          in the GenomicRanges package.

+

+    \item The \code{\link[GenomicFeatures]{makeTranscriptDbFromGFF}}

+          function and the \link[GenomicFeatures]{TranscriptDb} class

+          in the GenomicFeatures package.

+

+    \item The \link{SplicingGraphs} class.

+

+    \item \code{\link{plotTranscripts}} for plotting a set of transcripts

+          along genomic coordinates.

     \item \code{\link{countReads}} for assigning reads to the edges of a

           \link{SplicingGraphs} object and summarizing them.

@@ -70,9 +62,7 @@ suppressWarnings(

 )

 ## Plot all the transcripts in the gene model:

-if (interactive()) {

-  plotTranscripts(txdb)

-}

+plotTranscripts(txdb)

 ## ---------------------------------------------------------------------

 ## B. LOAD THE TOY READS AS A GappedAlignments OBJECT AND PLOT THEM

@@ -84,19 +74,8 @@ toy_reads_sam()

 toy_reads_bam()

 gal <- readGappedAlignments(toy_reads_bam(), use.names=TRUE)

-## Plot the reads:

-if (interactive()) {

-  ## All of them:

-  plotToyReads(gal, txdb)

-  ## The first 11 only:

-  plotToyReads(head(gal, n=11), txdb)

-  ## The rest of them:

-  plotToyReads(tail(gal, n=-11), txdb)

-  ## Reads 21 to 26:

-  plotToyReads(gal[21:26], txdb)

-  ## Read 26 only:

-  plotToyReads(gal[26], txdb)

-}

+plotTranscripts(txdb, reads=gal)

+plotTranscripts(txdb, reads=gal, from=1, to=320)

 ## ---------------------------------------------------------------------

 ## C. FIND THE OVERLAPS BETWEEN THE TOY READS AND THE TOY GENE MODEL