[Vennerable-commits] r39 - in pkg/Vennerable: . R inst/doc tests

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sun Aug 2 13:05:58 CEST 2009 

Author: js229
Date: 2009-08-02 13:05:56 +0200 (Sun, 02 Aug 2009)
New Revision: 39

Modified:
   pkg/Vennerable/DESCRIPTION
   pkg/Vennerable/R/02TissueDrawing.R
   pkg/Vennerable/R/03VennDrawing.R
   pkg/Vennerable/inst/doc/TissueDrawingTest.Rnw
   pkg/Vennerable/inst/doc/TissueDrawingTest.pdf
   pkg/Vennerable/inst/doc/Venn.Rnw
   pkg/Vennerable/tests/bug0521JuneAprilMay.R
Log:
fix bug 521 probably

Modified: pkg/Vennerable/DESCRIPTION
===================================================================
--- pkg/Vennerable/DESCRIPTION	2009-08-01 23:34:10 UTC (rev 38)
+++ pkg/Vennerable/DESCRIPTION	2009-08-02 11:05:56 UTC (rev 39)
@@ -1,6 +1,6 @@
 Package: Vennerable
 Title: Venn and Euler area-proportional diagrams
-Version: 1.0 
+Version: 2.0 
 Author: Jonathan Swinton
 Description: A package for drawing various species of Venn diagrams.
 Maintainer: Jonathan Swinton <jonathan at swintons.net>

Modified: pkg/Vennerable/R/02TissueDrawing.R
===================================================================
--- pkg/Vennerable/R/02TissueDrawing.R	2009-08-01 23:34:10 UTC (rev 38)
+++ pkg/Vennerable/R/02TissueDrawing.R	2009-08-02 11:05:56 UTC (rev 39)
@@ -979,9 +979,9 @@
 	centroid.xy <- matrix(c(cx,cy),ncol=2)
 }
 
-.PlotFace.TissueDrawing <- function(drawing,faceName,dx=0.05,gp=gpar()) {
+.PlotFace.TissueDrawing <- function(drawing,faceName,dx=0.05,gp=gpar(),doDarkMatter=FALSE) {
 #cat(faceName,"\n")
-	if (faceName=="DarkMatter") {
+	if (!doDarkMatter & faceName=="DarkMatter") {
 		return()
 	} 
 	all.xy <- .face.toxy(drawing,faceName,dx=dx)
@@ -1324,6 +1324,9 @@
 			# so further subdivision takes us back out of the Set
 			newFaceSigP <- inFaceSignature 
 			newFaceSigM <- paste(substr(inFaceSignature ,1,nSets-1),"0",sep="")
+	#		if (newFaceSigM==paste(rep("0",nSets),collapse="")) {
+	#			newFaceSigM <- "DarkMatter"
+	#		}
 		}
 	
 	}
@@ -2006,9 +2009,7 @@
 		# then negative ones
 		if (fedges[1]==inneg){ fedges <- fedges[c(2:length(fedges),1)] }
 		revName <- paste("-",newEdgeName,sep="")
-#if (fname=="10") {cat(sprintf("(%s): %s, %s -> %s\n",paste(fedges,collapse=","),inneg,outneg,revName))}
 		fedges <- spliceinstead(fedges,c(outneg,inneg),revName)
-#if (fname=="10") {cat(sprintf("(%s)\n",paste(fedges,collapse=",")))}
 		drawing at faceList[[fname]] <- fedges
 	}
 	drawing at nodeList[[inedge at to]] <- NULL
@@ -2016,7 +2017,10 @@
 }
 
 .merge.faces.invisibly.split <- function(diagram) {
-	fsigs <- data.frame(cbind(Name=unlist(.faceNames(diagram)),Signature=unlist(.faceSignatures(diagram))),stringsAsFactors=FALSE);rownames(fsigs)<- 1:nrow(fsigs)
+	fsigs <- data.frame(cbind(Name=unlist(.faceNames(diagram)),Signature=unlist(.faceSignatures(diagram))),stringsAsFactors=FALSE);
+	rownames(fsigs)<- 1:nrow(fsigs)
+	nSets <- unique(nchar(setdiff(fsigs$Signature,"DarkMatter")))
+	fsigs$Signature[fsigs$Signature==paste(rep("0",nSets),collapse="")] <- "DarkMatter"
 	w <- lapply(split(fsigs$Name,fsigs$Signature),length)
 	w <- w[w>1]
 	if (length(w)>0) {
@@ -2034,7 +2038,6 @@
 			firstVisibleIx <- min(which(faceVisible1))
 			firstVisibleFrom <- faceEdges1[[firstVisibleIx ]]@from
 			diagram<- .startFaceAtPoint(diagram,wnames[1],firstVisibleFrom )
-			#diagram<- .startFaceAtPoint(diagram,wnames[2],firstVisibleFrom )
 			faceEdges1 <- .face.to.faceEdges(diagram,wnames[1])
 			faceVisible1 <- sapply(faceEdges1,function(x)x at visible)	
 			faceEdges2 <- .face.to.faceEdges(diagram,wnames[2])

Modified: pkg/Vennerable/R/03VennDrawing.R
===================================================================
--- pkg/Vennerable/R/03VennDrawing.R	2009-08-01 23:34:10 UTC (rev 38)
+++ pkg/Vennerable/R/03VennDrawing.R	2009-08-02 11:05:56 UTC (rev 39)
@@ -193,7 +193,7 @@
 
 PlotVennGeometry <- function(C3,gpList,show=list(FaceText="weight")) {
 	show.default <- list(universe=TRUE,Sets=TRUE,SetLabels=TRUE,
-		dark.matter=FALSE,
+		DarkMatter=FALSE,
 		Faces=TRUE,
 		FaceText="weight")
 	unshown <- names(show)[! names(show) %in% names(show.default)]
@@ -216,6 +216,9 @@
 	if(show.default$universe) {
 		PlotUniverse(C3)
 	}
+	if(show.default$DarkMatter) {
+		PlotDarkMatter(C3)
+	}
 	if (show.default$Faces) {
 		PlotFaces(C3,gp=gp[["Face"]])
 	}
@@ -229,7 +232,7 @@
 	if (length(show.default$FaceText)>0) {
 		PlotIntersectionText(C3,element.plot=show.default$FaceText,
 			gp=gp[["FaceText"]],
-			show.dark.matter=show.default$dark.matter)	
+			show.dark.matter=show.default$DarkMatter)	
 	}
 
 	UpViewports()	
@@ -337,6 +340,10 @@
 	pushViewport(viewport(name="Vennvp",layout.pos.row=1,layout.pos.col=1,xscale=xrange,yscale=yrange))
 	}
 
+PlotDarkMatter <- function(VD) {
+	ur <- UniverseRange(VD)
+	grey <- brewer.pal(8,"Greys")[2]
+	grid.polygon(x=ur[c(1,1,2,2),1],y=ur[c(1,2,2,1),2],gp=gpar(fill=grey))
+	.PlotFace.TissueDrawing(VD,"DarkMatter",gp=gpar(fill="white"),doDarkMatter=TRUE)
+	}
 
-
-

Modified: pkg/Vennerable/inst/doc/TissueDrawingTest.Rnw
===================================================================
--- pkg/Vennerable/inst/doc/TissueDrawingTest.Rnw	2009-08-01 23:34:10 UTC (rev 38)
+++ pkg/Vennerable/inst/doc/TissueDrawingTest.Rnw	2009-08-02 11:05:56 UTC (rev 39)
@@ -49,7 +49,14 @@
 
 <<loadmore,echo=FALSE>>=
 options(width=80)
-shoar <- function(VDI) {lapply(VDI at edgeList,function(lh){xy <- .edge.to.xy(lh); grid.lines(xy[,1],xy[,2],default.units="native",arrow=arrow())})}
+shoar <- function(VDI) {
+	res <- lapply(VDI at edgeList,function(lh){
+		xy <- .edge.to.xy(lh);
+	      grid.lines(xy[,1],xy[,2],default.units="native",arrow=arrow())
+		}
+	)
+	invisible(res)
+}
 @
 
 \tableofcontents
@@ -805,7 +812,7 @@
 @
  \end{center}\end{figure}
 
-\section{One tangent point}
+\subsection{One tangent point}
 <<circ33a>>=
 r <- c( 1.261566 ,0.977205, 1.492705)
 x <- c(0.000000,  1.350138 ,-1.086542)
@@ -824,28 +831,28 @@
 makevp.eqsc(c(-3,3),c(-3,3))
 grid.xaxis()
 grid.yaxis()
-PlotFaces(TM3)
-PlotSetBoundaries(VDC1);PlotSetBoundaries(VDC2);
-PlotNodes(VDC1);PlotNodes(VDC2);
-.PlotFaceNames.TissueDrawing (TM3)
-PlotNodes(TM3)
-
+PlotFaces(TM)
+PlotSetBoundaries(VDC1);PlotSetBoundaries(VDC2);PlotSetBoundaries(VDC3);
+#PlotNodes(VDC1);PlotNodes(VDC2);PlotNodes(VDC3);
+.PlotFaceNames.TissueDrawing (TM)
+PlotNodes(TM)
+shoar(TM)
 @
  \end{center}\end{figure}
 
 
-\section{Three circles}
+\subsection{Three circles one tangent}
 <<circ33b>>=
 r <- c(  1.492705, 0.977205, 1.128379)
 x <- c(0.000000,  1.384666, -1.028597 )
  y <- c(1.49270533, -0.55257134, -0.02662434 )
 	centres <- matrix(c(x,y),ncol=2,byrow=FALSE)
-	VDC1 <- newTissueFromCircle(centres[1,],radius=r[1],Set=1,nodes=6); 
-	VDC2 <- newTissueFromCircle(centres[2,],radius=r[2],Set=2,nodes=2); 
-	TM <- addSetToDrawing (drawing1=VDC1,drawing2=VDC2,set2Name="Set2")
-	VDC3 <- newTissueFromCircle(centres[3,],radius=r[3],Set=3); 
-	TM3 <- addSetToDrawing (drawing1=TM,drawing2=VDC3,set2Name="Set3")
-	TV3 <- .merge.faces.invisibly.split(TM3)
+	VDC1b <- newTissueFromCircle(centres[1,],radius=r[1],Set=1,nodes=6); 
+	VDC2b <- newTissueFromCircle(centres[2,],radius=r[2],Set=2,nodes=2); 
+	TMb <- addSetToDrawing (drawing1=VDC1b,drawing2=VDC2b,set2Name="Set2")
+	VDC3b <- newTissueFromCircle(centres[3,],radius=r[3],Set=3); 
+	TM3b <- addSetToDrawing (drawing1=TMb,drawing2=VDC3b,set2Name="Set3")
+	TV3b <- .merge.faces.invisibly.split(TM3b)
 @
 \begin{figure}[H]\begin{center}
 
@@ -853,15 +860,10 @@
 grid.newpage();pushViewport(plotViewport(c(1,1,1,1)))
 makevp.eqsc(c(-3,3),c(-3,3))
 grid.xaxis();grid.yaxis()
-PlotFaces(TV3)
-PlotSetBoundaries(TV3)
-#PlotSetBoundaries(VDC3)
-#shoar(TM3)
+PlotFaces(TV3b)
+PlotSetBoundaries(TV3b)
+PlotNodes(TV3b)
 
-#PlotNodes(VDC1);PlotNodes(VDC2);
-#.PlotFaceNames.TissueDrawing (TM3)
-PlotNodes(TM3)
-
 @
  \end{center}\end{figure}
 

Modified: pkg/Vennerable/inst/doc/TissueDrawingTest.pdf
===================================================================
--- pkg/Vennerable/inst/doc/TissueDrawingTest.pdf	2009-08-01 23:34:10 UTC (rev 38)
+++ pkg/Vennerable/inst/doc/TissueDrawingTest.pdf	2009-08-02 11:05:56 UTC (rev 39)
@@ -91,43 +91,43 @@
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/vennerable -r 39

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