@@ -2,7 +2,7 @@ Package: Rgraphviz

 Title: Provides plotting capabilities for R graph objects

 Description: Interfaces R with the AT and T graphviz library for

         plotting R graph objects from the graph package.

-Version: 2.13.1

+Version: 2.27.0

 Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("cre", "aut"),

                     email = "kasperdanielhansen@gmail.com"),

              person("Jeff", "Gentry", role = "aut"),

@@ -21,11 +21,7 @@ Imports: stats4,

 	 grDevices

 Suggests: RUnit,

 	  BiocGenerics,

-	  knitr,

-	  rmarkdown,

-	  BiocStyle,

 	  XML

-VignetteBuilder: knitr

 SystemRequirements: optionally Graphviz (>= 2.16)

 GraphvizDetails: Graphviz 2.28.0

 License: EPL

@@ -46,4 +42,3 @@ Collate: AllGenerics.R

 	 writers.R

 	 zzz.R

 biocViews: GraphAndNetwork, Visualization

-URL: https://github.com/kasperdanielhansen/Rgraphviz

@@ -4,12 +4,7 @@ setMethod("getPoints", "xyPoint", function(object) c(object@x, object@y))

 setMethod("show", "xyPoint", function(object)

           cat(paste("x: ", object@x, ", y: ", object@y, "\n", sep="")))

-setMethod("labelText", "AgTextLabel", function(object) {

-    text <- object@labelText

-    text <- gsub('\\n', '\n', text, fixed=T)

-    text <- gsub('\\r', '\r', text, fixed=T) # only these two as per Graphviz lib/common/labels.c:make_simple_label

-    return(text)

-})

+setMethod("labelText", "AgTextLabel", function(object) object@labelText)

 setMethod("labelColor", "AgTextLabel", function(object) object@labelColor)

 setMethod("labelLoc", "AgTextLabel", function(object) object@labelLoc)

 setMethod("labelJust", "AgTextLabel", function(object) object@labelJust)

@@ -1,4 +1,4 @@

-graphLayout <- function(graph, layoutType=graph@layoutType, size=NULL)

+graphLayout <- function(graph, layoutType=graph@layoutType)

 {

     if (is(graph,"graph"))

         stop("Please use function agopen() for graph objects")

@@ -6,9 +6,9 @@ graphLayout <- function(graph, layoutType=graph@layoutType, size=NULL)

     if (!is(graph,"Ragraph"))

         stop("Object is not of class Ragraph")

-    if ( graph@layoutType != layoutType || !graph@laidout || !is.null(size)) {

+    if ( graph@layoutType != layoutType || !graph@laidout ) {

         graph@layoutType <- layoutType

-        z <- .Call("Rgraphviz_doLayout", graph, layoutType, size,

+        z <- .Call("Rgraphviz_doLayout", graph, layoutType,

                    PACKAGE="Rgraphviz");

     } else {

         z <- graph

@@ -12,7 +12,6 @@ setMethod("plot", "graph",

         warning("graph has zero nodes; cannot layout\n")

         return(invisible(x))

     }

-

     if (missing(y)) y <- "dot"

     recipEdges <- match.arg(recipEdges)

@@ -30,83 +29,81 @@ setMethod("plot", "Ragraph",

            main=NULL, cex.main=NULL, col.main="black",

            sub=NULL, cex.sub=NULL, col.sub="black",

            drawNode=drawAgNode, xlab, ylab, mai) {

-

-    if ( missing(y) ) y <- x@layoutType

-    x <- graphLayout(x, y, sprintf("%f,%f", par("pin")[1], par("pin")[2]))

-    

-    plot.new()

-    

-    bg <- if ( x@bg != "" ) x@bg else par("bg")

-    fg <- if ( x@fg != "" ) x@fg else par("fg")

-    oldpars <- par(bg = bg, fg = fg)

-    on.exit(par(oldpars), add = TRUE)

-    

-    if (missing(mai)) {

-        mheight <- if(!is.null(main) && nchar(main) > 0)

-            sum(strheight(main, "inches", cex.main)) + 0.3 else 0.1

-        sheight <- if(!is.null(sub) && nchar(sub) > 0)

-            sum(strheight(main, "inches", cex.sub)) + 0.2 else 0.1

-        mai <- c(sheight, 0, mheight, 0)

-    }

-    oldpars <- par(mai = mai)

-    on.exit(par(oldpars), add = TRUE)

-    if(!is.null(sub)||!is.null(main))

-        title(main, sub, cex.main = cex.main, col.main = col.main,

-              cex.sub = cex.sub, col.sub = col.sub)

-    

-    ## layout graph

-    

-    ur <- upRight(boundBox(x))

-    bl <- botLeft(boundBox(x))

-    plot.window(xlim = c(getX(bl), getX(ur)),

-                ylim = c(getY(bl), getY(ur)),

-                log = "", asp = NA, ...)

-    

-    if(!missing(xlab) && !missing(ylab))

-        stop("Arguments 'xlab' and 'ylab' are not handled.")

-    

-    ## determine whether node labels fit into nodes and set "cex" accordingly

-    agn <- AgNode(x)

-    nodeDims <- sapply(agn, function(n) {

-        c(getNodeRW(n)+getNodeLW(n), getNodeHeight(n))

-    })

-    strDims  <- sapply(agn, function(n) {

-        s  <- labelText(txtLabel(n))

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

-            rv <- c(strwidth(" "), strheight(" "))

-        } else {

-            rv <- c(strwidth(s)*1.1, strheight(s)*1.4)

-        }

-        return(rv)

-    } )

-    cex <- min(nodeDims / strDims)

-    if(is.finite(cex) && cex > 0 ) {

-        oldpars <- par(cex=cex)

-        on.exit(par(oldpars), add = TRUE)

-    }

-    

-    ## draw

-    if (length(drawNode) == 1) {

-        lapply(agn, drawNode)

-    } else {

-        if (length(drawNode) == length(AgNode(x))) {

-            for (i in seq(along=drawNode)) {

-                drawNode[[i]](agn[[i]])

-            }

-        } else {

-            stop(paste("Length of the drawNode parameter is ", length(drawNode),

-                       ", it must be either length 1 or the number of nodes.", sep=""))

-        }

-    }

-    

-    ## Use the smallest node radius as a means to scale the size of

-    ## the arrowheads -- in INCHES! see man page for "arrows",

-    arrowLen <- par("pin")[1] / diff(par("usr")[1:2]) * min(nodeDims) / pi

-    

-    ## Plot the edges

-    lapply(AgEdge(x), lines, len=arrowLen, edgemode=edgemode, ...)

-    

-    invisible(x)

+      ## layout graph

+      if ( missing(y) ) y <- x@layoutType

+      x <- graphLayout(x, y)

+

+      plot.new()

+

+      bg <- if ( x@bg != "" ) x@bg else par("bg")

+      fg <- if ( x@fg != "" ) x@fg else par("fg")

+      oldpars <- par(bg = bg, fg = fg)

+      on.exit(par(oldpars), add = TRUE)

+      

+      if (missing(mai)) {

+          mheight <- if(!is.null(main) && nchar(main) > 0)

+              sum(strheight(main, "inches", cex.main)) + 0.3 else 0.1

+          sheight <- if(!is.null(sub) && nchar(sub) > 0)

+              sum(strheight(main, "inches", cex.sub)) + 0.2 else 0.1

+          mai <- c(sheight, 0, mheight, 0)

+      }

+      oldpars <- par(mai = mai)

+      on.exit(par(oldpars), add = TRUE)

+      if(!is.null(sub)||!is.null(main))

+          title(main, sub, cex.main = cex.main, col.main = col.main, 

+                cex.sub = cex.sub, col.sub = col.sub)

+      

+      ur <- upRight(boundBox(x))

+      bl <- botLeft(boundBox(x))

+      plot.window(xlim = c(getX(bl), getX(ur)),

+                  ylim = c(getY(bl), getY(ur)),

+                  log = "", asp = NA, ...)

+      

+      if(!missing(xlab) && !missing(ylab))

+          stop("Arguments 'xlab' and 'ylab' are not handled.")

+      

+      ## determine whether node labels fit into nodes and set "cex" accordingly

+      agn <- AgNode(x)

+      nodeDims <- sapply(agn, function(n) {

+          c(getNodeRW(n)+getNodeLW(n), getNodeHeight(n))

+      })

+      strDims  <- sapply(agn, function(n) {

+          s  <- labelText(txtLabel(n))

+          if(length(s)==0) {

+              rv <- c(strwidth(" "), strheight(" "))

+          } else {

+              rv <- c(strwidth(s)*1.1, strheight(s)*1.4)

+          }

+          return(rv)

+      } )

+      cex <- min(nodeDims / strDims)

+      if(is.finite(cex) && cex > 0 ) {

+          oldpars <- par(cex=cex)

+          on.exit(par(oldpars), add = TRUE)

+      }

+      

+      ## draw

+      if (length(drawNode) == 1) {

+          lapply(agn, drawNode)

+      } else {

+          if (length(drawNode) == length(AgNode(x))) {

+              for (i in seq(along=drawNode)) {

+                  drawNode[[i]](agn[[i]])

+              }

+          } else {

+              stop(paste("Length of the drawNode parameter is ", length(drawNode),

+                         ", it must be either length 1 or the number of nodes.", sep=""))

+          }

+      }

+

+      ## Use the smallest node radius as a means to scale the size of

+      ## the arrowheads -- in INCHES! see man page for "arrows", 

+      arrowLen <- par("pin")[1] / diff(par("usr")[1:2]) * min(nodeDims) / pi

+      

+      ## Plot the edges

+      lapply(AgEdge(x), lines, len=arrowLen, edgemode=edgemode, ...)

+      

+      invisible(x)

 })

@@ -124,7 +121,7 @@ drawAgNode <- function(node) {

   shape <- shape(node)

   ## Normal Rgraphviz defaults to circle, but DOT defaults to ellipse

-  if (shape =="") shape <- "ellipse"

+  if (shape =="") shape <- "ellipse" 

   if (fg == "") fg <- "black"

   bg <- fillcolor(node)

@@ -138,8 +135,8 @@ drawAgNode <- function(node) {

          "ellipse"   = ellipse(x=nodeX, y=nodeY, height=height, width=rad*2, fg=fg, bg=bg),

          "box"=,

          "rect"=,

-         "rectangle" = rect(nodeX-lw, nodeY-(height/2),

-			    nodeX+rw, nodeY+(height/2),

+         "rectangle" = rect(nodeX-lw, nodeY-(height/2), 

+			    nodeX+rw, nodeY+(height/2), 

 			    col=bg, border=fg),

          "plaintext"= { if (style == "filled")

                           rect(nodeX-lw, nodeY-(height/2),

@@ -3,8 +3,9 @@

 This is the developer version of Bioconductor package [Rgraphviz](http://bioconductor.org/packages/devel/bioc/html/Rgraphviz.html).  Install in R as:

 ```r

-source('http://bioconductor.org/biocLite.R')

-biocLite('Rgraphviz')

+if (!requireNamespace("BiocManager", quietly=TRUE))

+    install.packages("BiocManager")

+BiocManager::install('Rgraphviz')

 ```

 # Additional installation tips

@@ -72,7 +72,10 @@ V <- letters[1:10]

 M <- 1:4

 g1 <- randomGraph(V, M, .2)

 z <- agopenSimple(g1,name="foo")

-plot(z, "twopi")

+if(graphvizVersion() >= "2.10") {

+  ## This example will only run with Graphviz >= 2.10

+  plot(z, "twopi")

+}

 }

 \keyword{graphs}

@@ -6,18 +6,16 @@

   perform a libgraph layout on the graph locations.

 }

 \usage{

-graphLayout(graph, layoutType=graph@layoutType, size=NULL)

+graphLayout(graph, layoutType=graph@layoutType)

 }

 \arguments{

   \item{graph}{An object of type \code{Ragraph}}

   \item{layoutType}{layout algorithm to use}

-  \item{size}{Size in inches, given as string of the form "width,height". Can be NULL.}

 }

 \details{

-  If the graph has already been laid out and \code{size} is \code{NULL},

-  this function merely returns its parameter.  Otherwise, it will perform

-  a libgraph layout and retrieve the appropriate location information.

-  If \code{size} is not NULL, the layout will try to match the given size.

+  If the graph has already been laid out, this function merely returns

+  its parameter.  Otherwise, it will perform a libgraph layout and

+  retrieve the appropriate location information.

 }

 \value{

   A laid out object of type \code{Ragraph}.

@@ -28,7 +26,7 @@ graphLayout(graph, layoutType=graph@layoutType, size=NULL)

 V <- letters[1:10]

 M <- 1:4

 g1 <- randomGraph(V, M, .2)

-z <- agopen(g1, "foo", layout=FALSE)

+z <- agopen(g1,"foo",layout=FALSE)

 x <- z

 a <- graphLayout(z)

 }

@@ -4,7 +4,7 @@ static const R_CallMethodDef R_CallDef[] = {

              {"Rgraphviz_agread", (DL_FUNC)&Rgraphviz_agread, 1},

              {"Rgraphviz_agwrite", (DL_FUNC)&Rgraphviz_agwrite, 2},

              {"Rgraphviz_agopen", (DL_FUNC)&Rgraphviz_agopen, 6},

-             {"Rgraphviz_doLayout", (DL_FUNC)&Rgraphviz_doLayout, 3},

+             {"Rgraphviz_doLayout", (DL_FUNC)&Rgraphviz_doLayout, 2},

              {"Rgraphviz_graphvizVersion", (DL_FUNC)&Rgraphviz_graphvizVersion, 0},

              {"Rgraphviz_bezier", (DL_FUNC)&Rgraphviz_bezier, 3},

@@ -34,7 +34,7 @@ SEXP Rgraphviz_agwrite(SEXP, SEXP);

 SEXP Rgraphviz_bezier(SEXP, SEXP, SEXP);

 SEXP Rgraphviz_buildNodeList(SEXP, SEXP, SEXP, SEXP);

 SEXP Rgraphviz_buildEdgeList(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);

-SEXP Rgraphviz_doLayout(SEXP, SEXP, SEXP);

+SEXP Rgraphviz_doLayout(SEXP, SEXP);

 SEXP Rgraphviz_graphvizVersion(void);

 SEXP Rgraphviz_init(void);

@@ -94,9 +94,9 @@ SEXP getEdgeLocs(Agraph_t *g) {

             SET_SLOT(curEP, Rf_install("head"), Rgraphviz_ScalarStringOrNull(head->name));

             /* TODO: clean up the use of attrs: dir, arrowhead, arrowtail.

-             * the following are for interactive plotting in R-env, not needed

+             * the following are for interactive plotting in R-env, not needed 

              * for output to files.  The existing codes set "dir"-attr, but use

-             * "arrowhead"/"arrowtail" instead.  Quite confusing.

+             * "arrowhead"/"arrowtail" instead.  Quite confusing.  

              */

             SET_SLOT(curEP, Rf_install("dir"), Rgraphviz_ScalarStringOrNull(agget(edge, "dir")));

             SET_SLOT(curEP, Rf_install("arrowhead"), Rgraphviz_ScalarStringOrNull(agget(edge, "arrowhead")));

@@ -116,7 +116,7 @@ SEXP getEdgeLocs(Agraph_t *g) {

             if (edge->u.label != NULL) {

                 PROTECT(curLab = NEW_OBJECT(labClass));

                 SET_SLOT(curLab, Rf_install("labelText"),

-                         Rgraphviz_ScalarStringOrNull(ED_label(edge)->text));

+                         Rgraphviz_ScalarStringOrNull(ED_label(edge)->u.txt.para->str));

                 /* Get the X/Y location of the label */

                 PROTECT(curXY = NEW_OBJECT(xyClass));

 #if GRAPHVIZ_MAJOR == 2 && GRAPHVIZ_MINOR > 20

@@ -196,10 +196,10 @@ SEXP getNodeLayouts(Agraph_t *g) {

         PROTECT(curLab = NEW_OBJECT(labClass));

-        if (ND_label(node)  == NULL) {

-        } else if (ND_label(node)->u.txt.para != NULL) {

+	if (ND_label(node)  == NULL) {

+	} else if (ND_label(node)->u.txt.para != NULL) {

             SET_SLOT(curLab, Rf_install("labelText"),

-                     Rgraphviz_ScalarStringOrNull(ND_label(node)->text));

+                     Rgraphviz_ScalarStringOrNull(ND_label(node)->u.txt.para->str));

             snprintf(tmpString, 2, "%c",ND_label(node)->u.txt.para->just);

             SET_SLOT(curLab, Rf_install("labelJust"), Rgraphviz_ScalarStringOrNull(tmpString));

@@ -238,7 +238,7 @@ SEXP getNodeLayouts(Agraph_t *g) {

 static char *layouts[] = { "dot", "neato", "twopi", "circo", "fdp"};

 */

-SEXP Rgraphviz_doLayout(SEXP graph, SEXP layoutType, SEXP size) {

+SEXP Rgraphviz_doLayout(SEXP graph, SEXP layoutType) {

     /* Will perform a Graphviz layout on a graph */

     Agraph_t *g;

@@ -249,13 +249,12 @@ SEXP Rgraphviz_doLayout(SEXP graph, SEXP layoutType, SEXP size) {

     CHECK_Rgraphviz_graph(slotTmp);

     g = R_ExternalPtrAddr(slotTmp);

-    if (size != R_NilValue) {

-        agsafeset(g, "size", CHAR(STRING_ELT(size, 0)), NULL);

-    }

-

     /* Call the appropriate Graphviz layout routine */

     gvLayout(gvc, g, CHAR(STRING_ELT(layoutType, 0)));

+    /* Call the appropriate Graphviz layout routine */

+    gvLayout(gvc, g, CHAR(STRING_ELT(layoutType, 0)));

+    

     /*

     if (!isInteger(layoutType))

         error("layoutType must be an integer value");