@@ -13,7 +13,7 @@ Depends: BiocGenerics, IRanges (>= 1.17.31), GenomicRanges,

 Imports: methods, utils, igraph,

 	 BiocGenerics, IRanges, GenomicRanges,

 	 graph, Rgraphviz, GenomicFeatures, Rsamtools

-Suggests: Gviz, TxDb.Mmusculus.UCSC.mm9.knownGene, RUnit

+Suggests: igraph, Gviz, TxDb.Mmusculus.UCSC.mm9.knownGene, RUnit

 Collate: utils.R

 	 splicingGraphs.R

 	 countReads.R

@@ -420,20 +420,20 @@ setMethod("Sgdf", "data.frame",

 ###

 setGeneric("Sgraph", signature="x",

-    function(x, gene_id=NA, keep.dup.edges=FALSE, as.Ragraph=FALSE)

+    function(x, gene_id=NA, keep.dup.edges=FALSE, as.igraph=FALSE)

         standardGeneric("Sgraph")

 )

 setMethod("Sgraph", "ANY",

-    function(x, gene_id=NA, keep.dup.edges=FALSE, as.Ragraph=FALSE)

+    function(x, gene_id=NA, keep.dup.edges=FALSE, as.igraph=FALSE)

     {

         sgdf <- Sgdf(x, gene_id=gene_id, keep.dup.edges=keep.dup.edges)

-        Sgraph(sgdf, as.Ragraph=as.Ragraph)

+        Sgraph(sgdf, as.igraph=as.igraph)

     }

 )

 setMethod("Sgraph", "data.frame",

-    function(x, gene_id=NA, keep.dup.edges=FALSE, as.Ragraph=FALSE)

+    function(x, gene_id=NA, keep.dup.edges=FALSE, as.igraph=FALSE)

     {

         if (!identical(gene_id, NA))

             stop("the 'gene_id' arg is not supported ",

@@ -442,12 +442,12 @@ setMethod("Sgraph", "data.frame",

             stop("the 'keep.dup.edges' arg is not supported ",

                  "when 'x' is a data.frame")

         igraph <- .make_igraph_from_Sgdf0(x)

-        Sgraph(igraph, as.Ragraph=as.Ragraph)

+        Sgraph(igraph, as.igraph=as.igraph)

     }

 )

 setMethod("Sgraph", "DataFrame",

-    function(x, gene_id=NA, keep.dup.edges=FALSE, as.Ragraph=FALSE)

+    function(x, gene_id=NA, keep.dup.edges=FALSE, as.igraph=FALSE)

     {

         if (!identical(gene_id, NA))

             stop("the 'gene_id' arg is not supported ",

@@ -456,12 +456,12 @@ setMethod("Sgraph", "DataFrame",

             stop("the 'keep.dup.edges' arg is not supported ",

                  "when 'x' is a DataFrame")

         igraph <- .make_igraph_from_Sgdf(x)

-        Sgraph(igraph, as.Ragraph=as.Ragraph)

+        Sgraph(igraph, as.igraph=as.igraph)

     }

 )

 setMethod("Sgraph", "igraph",

-    function(x, gene_id=NA, keep.dup.edges=FALSE, as.Ragraph=FALSE)

+    function(x, gene_id=NA, keep.dup.edges=FALSE, as.igraph=FALSE)

     {

         if (!identical(gene_id, NA))

             stop("the 'gene_id' arg is not supported ",

@@ -469,10 +469,14 @@ setMethod("Sgraph", "igraph",

         if (!identical(keep.dup.edges, FALSE))

             stop("the 'keep.dup.edges' arg is not supported ",

                  "when 'x' is an igraph object")

-        if (!isTRUEorFALSE(as.Ragraph))

-            stop("'as.Ragraph' must be TRUE or FALSE")

-        if (!as.Ragraph)

+        if (!isTRUEorFALSE(as.igraph))

+            stop("'as.igraph' must be TRUE or FALSE")

+        if (as.igraph) {

+            ## Need to load the igraph package so the user can display, plot,

+            ## and manipulate the returned object.

+            library(igraph)

             return(x)  # no-op

+        }

         make_Ragraph_from_igraph(x)

     }

 )

@@ -575,11 +579,11 @@ Sgdf2 <- function(x, gene_id=NA)

 ### Same as Sgraph() except that uninformative nodes (i.e. SSids) are removed.

 ###

-Sgraph2 <- function(x, gene_id=NA, as.Ragraph=FALSE)

+Sgraph2 <- function(x, gene_id=NA, as.igraph=FALSE)

 {

     if (!is(x, "DataFrame"))

         x <- Sgdf2(x, gene_id=gene_id)

-    Sgraph(x, as.Ragraph=as.Ragraph)

+    Sgraph(x, as.igraph=as.igraph)

 }

@@ -107,18 +107,24 @@ layout.Sgraph <- function(graph)

 .make_Ragraph_edgeAttrs_from_graphNEL <- function(graph_nel)

 {

     attr_names <- names(edgeDataDefaults(graph_nel))

-    edge_names <- edgeNames(graph_nel)

-    if (length(attr_names) == 0L || length(edge_names) == 0L)

-        return(list())

-    if (anyDuplicated(edge_names))

-        warning("graphNEL object has more than 1 edge between the same ",

-                "2 nodes. Plotting attributes for those edges (e.g. label, ",

-                "color, line width, line style, etc...) are likely to be ",

-                "wrong.")

     edge_data <- edgeData(graph_nel)

-    stopifnot(identical(.safeTranslateEdgeNames(names(edge_data)),

-                        edge_names))  # sanity check

-    names(edge_data) <- edge_names

+    edge_data_names <- names(edge_data)

+    if (length(attr_names) == 0L || length(edge_data_names) == 0L)

+        return(list())

+    if (anyDuplicated(edge_data_names))

+        warning("graph object has more than 1 edge between the same ",

+                "2 nodes. Because setting plotting attributes for those ",

+                "edges (e.g. label, color, line width, line style, etc...) ",

+                "is not fully supported yet, they will end up with the same ",

+                "attributes. Which is unlikely to be what you want.")

+    edge_data_names <- .safeTranslateEdgeNames(edge_data_names)

+

+    ## edgeNames() is broken on graphNEL objects that have more than 1 edge

+    ## between the same 2 nodes, hence the use of unique() in the sanity check.

+    edge_names <- edgeNames(graph_nel)

+    stopifnot(identical(unique(edge_data_names), edge_names))  # sanity check

+

+    names(edge_data) <- edge_data_names

     edge_attrs <- lapply(attr_names,

                          function(attr_name)

                              unlist(lapply(edge_data, `[[`, attr_name),

@@ -128,8 +134,8 @@ layout.Sgraph <- function(graph)

     is_null <- sapply(edge_attrs, is.null)

     edge_attrs <- edge_attrs[!is_null]

-    edge_fontsize <- rep.int("10", length(edge_names))

-    names(edge_fontsize) <- edge_names

+    edge_fontsize <- rep.int("10", length(edge_data_names))

+    names(edge_fontsize) <- edge_data_names

     edge_attrs$fontsize <- edge_fontsize

     edge_attrs

@@ -38,13 +38,13 @@ dim(TREM2sgdf)

 ## Plot the splicing graphs:

 library(Rgraphviz)

-plot(Sgraph(BAI1sgdf, as.Ragraph=TRUE))

-plot(Sgraph(CYB561sgdf, as.Ragraph=TRUE))

-plot(Sgraph(DAPL1sgdf, as.Ragraph=TRUE))

-plot(Sgraph(ITGB8sgdf, as.Ragraph=TRUE))

-plot(Sgraph(KIAA0319Lsgdf, as.Ragraph=TRUE))

-plot(Sgraph(LGSNsgdf, as.Ragraph=TRUE))

-plot(Sgraph(MKRN3sgdf, as.Ragraph=TRUE))

-plot(Sgraph(ST14sgdf, as.Ragraph=TRUE))

-plot(Sgraph(TREM2sgdf, as.Ragraph=TRUE))

+plot(Sgraph(BAI1sgdf))

+plot(Sgraph(CYB561sgdf))

+plot(Sgraph(DAPL1sgdf))

+plot(Sgraph(ITGB8sgdf))

+plot(Sgraph(KIAA0319Lsgdf))

+plot(Sgraph(LGSNsgdf))

+plot(Sgraph(MKRN3sgdf))

+plot(Sgraph(ST14sgdf))

+plot(Sgraph(TREM2sgdf))

 }

@@ -50,7 +50,7 @@ tx_by_gn <- transcriptsBy(toy_genes_txdb, by="gene")

 ## Compute the splicing graphs (1 graph per gene):

 ex_by_tx2 <- splicingGraphs(ex_by_tx, tx_by_gn)

 names(ex_by_tx2)

-plot(Sgraph(ex_by_tx2, "geneA", as.Ragraph=TRUE))

+plot(Sgraph(ex_by_tx2, gene_id="geneA"))

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

 ## 2. Load toy reads and find the hits that are "compatible" with the

@@ -91,7 +91,7 @@ UATXHcount <- countSubjectHits(ov2)

 mcols(ex_by_tx2)$UATXHcount <- UATXHcount

 names(ex_by_tx2)

-plot(Sgraph(ex_by_tx2, "geneA", as.Ragraph=TRUE))

+plot(Sgraph(ex_by_tx2, gene_id="geneA"))

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

 ## 4. Count nb of compatible hits per edge (NOTE: the same read can be

@@ -106,5 +106,5 @@ ex_by_tx2 <- assignSubfeatureHits(grl, ex_by_tx2, ov1, ignore.strand=TRUE)

 in_by_tx2 <- psetdiff(range(ex_by_tx2), ex_by_tx2)

 in_by_tx2 <- assignSubfeatureHits(grl, in_by_tx2, ov1, ignore.strand=TRUE)

-Sgdf(ex_by_tx2, "geneA", inbytx=in_by_tx2)

+Sgdf(ex_by_tx2, gene_id="geneA", inbytx=in_by_tx2)

 }

@@ -42,10 +42,10 @@ splicingGraphs(exbytx, grouping=NULL, check.introns=TRUE)

 Spath(x, gene_id=NA)

 UATXHcount(x, gene_id=NA)

 Sgdf(x, gene_id=NA, UATXHcount=NULL, inbytx=NULL, keep.dup.edges=FALSE)

-Sgraph(x, gene_id=NA, keep.dup.edges=FALSE, as.Ragraph=FALSE)

+Sgraph(x, gene_id=NA, keep.dup.edges=FALSE, as.igraph=FALSE)

 uninformativeSSids(x, gene_id=NA)

 Sgdf2(x, gene_id=NA)

-Sgraph2(x, gene_id=NA, as.Ragraph=FALSE)

+Sgraph2(x, gene_id=NA, as.igraph=FALSE)

 }

 \arguments{

@@ -76,7 +76,7 @@ Sgraph2(x, gene_id=NA, as.Ragraph=FALSE)

   \item{keep.dup.edges}{

     TODO

   }

-  \item{as.Ragraph}{

+  \item{as.igraph}{

     TODO

   }

 }

@@ -199,14 +199,9 @@ sgdfA <- Sgdf(ex_by_tx2, gene_id="geneA")

 sgdfA

 if (interactive()) {

-  ## By default Sgraph() returns an igraph object so we need the igraph

-  ## package to plot it.

-  library(igraph)

+  ## Edges are labeled with the transcript ids (or names), in blue.

+  ## The green arrows are edges corresponding to exons.

   plot(Sgraph(sgdfA))

-

-  ## Plotting an Ragraph (Rgraphviz package) instead of an igraph object.

-  ## The graphviz layout engine seems to to a better job...

-  plot(Sgraph(sgdfA, as.Ragraph=TRUE))

 }

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

@@ -240,9 +235,9 @@ if (FALSE) {

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

 if (interactive()) {

-  plot(Sgraph(ex_by_tx2, gene_id="geneB", as.Ragraph=TRUE))

-  plot(Sgraph(ex_by_tx2, gene_id="geneC", as.Ragraph=TRUE))

-  plot(Sgraph(ex_by_tx2, gene_id="geneD", as.Ragraph=TRUE))

-  plot(Sgraph(ex_by_tx2, gene_id="geneE", as.Ragraph=TRUE))

+  plot(Sgraph(ex_by_tx2, gene_id="geneB"))

+  plot(Sgraph(ex_by_tx2, gene_id="geneC"))

+  plot(Sgraph(ex_by_tx2, gene_id="geneD"))

+  plot(Sgraph(ex_by_tx2, gene_id="geneE"))

 }

 }