[Vennerable-commits] r58 - in pkg/Vennerable: R inst/doc man tests

[noreply at r-forge.r-project.org]

Author: js229
Date: 2009-09-24 00:57:05 +0200 (Thu, 24 Sep 2009)
New Revision: 58

Modified:
   pkg/Vennerable/R/03VennDrawing.R
   pkg/Vennerable/R/AWFE.R
   pkg/Vennerable/R/ChowRuskey.R
   pkg/Vennerable/R/Circles.R
   pkg/Vennerable/R/FourEllipses.R
   pkg/Vennerable/R/ThreeSquares.R
   pkg/Vennerable/R/Triangles.R
   pkg/Vennerable/inst/doc/TissueDrawingTest.Rnw
   pkg/Vennerable/inst/doc/TissueDrawingTest.pdf
   pkg/Vennerable/inst/doc/Venn.Rnw
   pkg/Vennerable/inst/doc/Venn.pdf
   pkg/Vennerable/inst/doc/VennDrawingTest.Rnw
   pkg/Vennerable/inst/doc/VennDrawingTest.pdf
   pkg/Vennerable/man/VennDrawing-class.Rd
   pkg/Vennerable/tests/bug0522CR0100.R
   pkg/Vennerable/tests/bug0524CR1100.R
Log:
mainly rewrite of SetLabels and FaceLabels handling and improved 4-squares label positioning

Modified: pkg/Vennerable/R/03VennDrawing.R
===================================================================
--- pkg/Vennerable/R/03VennDrawing.R	2009-09-18 17:14:09 UTC (rev 57)
+++ pkg/Vennerable/R/03VennDrawing.R	2009-09-23 22:57:05 UTC (rev 58)
@@ -12,16 +12,22 @@
 
 ################################################
 setGeneric("PlotUniverse",function(object,gp){standardGeneric("PlotUniverse")})
-setGeneric("IntersectionMidpoints",function(object){standardGeneric("IntersectionMidpoints")}) 
-setGeneric("SetLabelPositions",function(object){standardGeneric("SetLabelPositions")}) 
+#setGeneric("IntersectionMidpoints",function(object){standardGeneric("IntersectionMidpoints")}) 
+#setGeneric("SetLabelPositions",function(object){standardGeneric("SetLabelPositions")}) 
 setGeneric("Areas",function(object){standardGeneric("Areas")}) 
 setGeneric("ComputeAreas",function(object,nintervals){standardGeneric("ComputeAreas")}) 
 setGeneric("VisibleRange",function(object){standardGeneric("VisibleRange")}) 
 setGeneric("UniverseRange",function(object){standardGeneric("UniverseRange")}) 
+setGeneric("VennSetSetLabels",function(object,SetLabels){standardGeneric("VennSetSetLabels")}) 
+setGeneric("VennGetSetLabels",function(object){standardGeneric("VennGetSetLabels")}) 
+setGeneric("VennSetFaceLabels",function(object,FaceLabels){standardGeneric("VennSetFaceLabels")}) 
+setGeneric("VennGetFaceLabels",function(object){standardGeneric("VennGetFaceLabels")}) 
 
 
-setClass("VennDrawing",representation("TissueDrawing","Venn",universe="matrix"))
 
+setClass("VennDrawing",representation("TissueDrawing","Venn",
+	universe="matrix",SetLabels="data.frame",FaceLabels="data.frame"))
+
 setMethod("show","VennDrawing",function(object) {
 	show(as(object,"Venn"))
 	show(as(object,"TissueDrawing"))
@@ -30,22 +36,29 @@
 
 setMethod("UniverseRange","VennDrawing",function(object)object at universe)
 # eg CircleDrawing overrides these methods:
-setMethod("VisibleRange","VennDrawing",function(object){
+setMethod("VisibleRange","TissueDrawing",function(object){
 	dxxy <- do.call("rbind",lapply(names(object at setList),.face.toxy,type="set",drawing=object))
 	apply(dxxy,2,range)
 })
 
-setMethod("SetLabelPositions","VennDrawing",function(object){
+.default.SetLabelPositions <- function(object){
 	yscale <- diff(VisibleRange(object)[,2]); smidge <- 0.01*yscale
 	sxxy <- lapply(names(object at setList),.face.toxy,type="set",drawing=object)
+	setNames <- VennSetNames(as(object,"Venn"))
 	smaxy <- do.call(rbind,lapply(sxxy,function(x){x[which(x[,2]==max(x[,2]))[1],] }))
 	VLabels <- data.frame(Label=rep("unset",nrow(smaxy)),x=NA,y=NA,hjust=I("left"),vjust=I("bottom"))
 	VLabels[,2:3] <- smaxy
-	VLabels$Label <- VennSetNames(as(object,"Venn"))
+	VLabels$Label <- setNames 
 	VLabels
 }
-)
 
+setMethod("VennSetSetLabels","VennDrawing",function(object,SetLabels) {object at SetLabels <- SetLabels; object})
+setMethod("VennGetSetLabels","VennDrawing",function(object) {object at SetLabels})
+setMethod("VennSetFaceLabels","VennDrawing",function(object,FaceLabels) {object at FaceLabels <- FaceLabels; object})
+setMethod("VennGetFaceLabels","VennDrawing",function(object) {object at FaceLabels})
+
+
+
 setMethod("PlotUniverse","VennDrawing", function(object,gp) {
 	if(missing(gp)) { gp <- NULL }
 	uv <- UniverseRange(object)
@@ -55,7 +68,7 @@
 )
 
 .square.universe <- function(object,doWeights=FALSE,smudge=0.05) {
-	if (doWeights) {
+	if (FALSE & doWeights) { # never attempt to weight the Dark Matter for now
 		# minimal square box 
 		minimal.square.universe.area <- diff(VisibleRange(object)[,1])*diff(VisibleRange(object)[,2])
 		V <- as(object,"Venn")
@@ -169,12 +182,18 @@
 	} else {
 		gp <- lapply(gp,function(agp){res<-agp;res$col<-"black";res$fill<-res$col;res})
 	}
+	Nsets <- NumberOfSets(drawing)
+	fontsize <- if (Nsets<=3) { 20 } else {10 }
+	gp <- lapply(gp,function(agp){res<-agp;res$fontsize<-fontsize;res})
 	gp
 }
 
 SetTextColours <- function(drawing) {
 	gp <- SetColours(drawing=drawing)
-	gp <- lapply(gp,function(agp){res<-agp;res$col<-"black";res$fill<-res$col;res})
+#	gp <- lapply(gp,function(agp){res<-agp;res$col<-"black";res$fill<-res$col;res})
+	Nsets <- NumberOfSets(drawing)
+	fontsize <- if (Nsets<=3) { 20 } else {10 }
+	gp <- lapply(gp,function(agp){res<-agp;res$fontsize<-fontsize;res})
 	gp
 }
 
@@ -201,7 +220,7 @@
 
 
 PlotVennGeometry <- function(C3,gpList,show=list(FaceText="weight")) {
-	show.default <- list(universe=TRUE,Sets=TRUE,SetLabels=TRUE,
+	show.default <- list(Universe=TRUE,Sets=TRUE,SetLabels=TRUE,
 		DarkMatter=FALSE,
 		Faces=TRUE,
 		FaceText="weight")
@@ -222,7 +241,7 @@
  	
 	CreateViewport(C3)
 	
-	if(show.default$universe) {
+	if(show.default$Universe) {
 		PlotUniverse(C3)
 	}
 	if(show.default$DarkMatter) {
@@ -252,7 +271,8 @@
 	if (missing(gp)) gp <- FaceTextColours(object)
 	V <- as(object,"Venn")
 	nSets <- NumberOfSets(V)
-	VI <- IntersectionMidpoints(object);rownames(VI) <- VI$FaceName
+	VI <- VennGetFaceLabels(object);
+	rownames(VI) <- VI$FaceName
 
 	
 	VI$Annotation <- ""
@@ -299,8 +319,7 @@
 	}
 }
 
-
-setMethod("IntersectionMidpoints","VennDrawing",function(object){	
+.default.FaceLabelPositions <- function(object){	
 	dm <-  dark.matter.signature(object)
 	ilabels <- data.frame(internalPointsofFaces(as(object,"TissueDrawing")))
 	colnames(ilabels) <- c("x","y")
@@ -314,7 +333,7 @@
 	df[df$Signature==dm,c("hjust")] <- c("right")
 	df[df$Signature==dm,c("vjust")] <- c("top")
 	df
-})
+}
 
 setMethod("Areas","VennDrawing",function(object) {
 	areas <- faceAreas(as(object,"TissueDrawing"))
@@ -325,9 +344,8 @@
 
 
 
-
 PlotSetLabels <- function(object,gp) {
-	VLabels <- SetLabelPositions(object)
+	VLabels <- VennGetSetLabels(object)
 	if(missing(gp)) gp <- SetColours(object)
 	if(nrow(VLabels)==0){ warning("Can't show Set labels"); return()}
 #	print(VLabels)

Modified: pkg/Vennerable/R/AWFE.R
===================================================================
--- pkg/Vennerable/R/AWFE.R	2009-09-18 17:14:09 UTC (rev 57)
+++ pkg/Vennerable/R/AWFE.R	2009-09-23 22:57:05 UTC (rev 58)
@@ -16,6 +16,10 @@
 	}
 	TM <- VennDiagrams[[type]][[n]]
 	VD <- new("VennDrawing",TM,V)
+	SetLabels <- .default.SetLabelPositions(VD)
+	VD <- VennSetSetLabels(VD,SetLabels)
+	FaceLabels <- .default.FaceLabelPositions(VD)
+	VD <- VennSetFaceLabels(VD,FaceLabels)
 	VD <- .square.universe(VD,doWeights=FALSE)
 	VD
 

Modified: pkg/Vennerable/R/ChowRuskey.R
===================================================================
--- pkg/Vennerable/R/ChowRuskey.R	2009-09-18 17:14:09 UTC (rev 57)
+++ pkg/Vennerable/R/ChowRuskey.R	2009-09-23 22:57:05 UTC (rev 58)
@@ -292,6 +292,7 @@
 	nncount <- sapply(nnsplit,function(x)length(x[x=="1"]))
 	regionNames [order(-nncount)]
 }
+
 compute.CR <- function(V,doWeights=TRUE) {
 	nSets <- NumberOfSets(V)
 	Vorig <- V
@@ -387,7 +388,11 @@
 
 	TD <- as(TD,"TissueDrawing")
 	VD <- new("VennDrawing",TD,Vorig)
+	SetLabels <- .default.SetLabelPositions(VD)
+	VD <- VennSetSetLabels(VD,SetLabels)
 	VD <- .square.universe(VD ,doWeights=doWeights)
+	FaceLabels <- .default.FaceLabelPositions(VD)
+	VD <- VennSetFaceLabels(VD,FaceLabels)
 	VD
 }
 

Modified: pkg/Vennerable/R/Circles.R
===================================================================
--- pkg/Vennerable/R/Circles.R	2009-09-18 17:14:09 UTC (rev 57)
+++ pkg/Vennerable/R/Circles.R	2009-09-23 22:57:05 UTC (rev 58)
@@ -5,7 +5,6 @@
 # r is radius of circle
 # d distance from origin
 
-setClass("CircleDrawing",representation("VennDrawing",radii="numeric",centres="matrix"))
 
 TwoCircles <- function(r,d,V) {
 	if (length(r) !=2 ) {
@@ -20,26 +19,32 @@
 	VDC1 <- newTissueFromCircle(centres[1,],radius=r[1],Set=1); 
 	VDC2 <- newTissueFromCircle(centres[2,],radius=r[2],Set=2); 
 	TM <- addSetToDrawing (drawing1=VDC1,drawing2=VDC2,set2Name="Set2",remove.points=TRUE)
-	new("CircleDrawing",TM,V,radii=r,centres=centres)
+	V2 <- new("VennDrawing",TM,V)
+	SetLabels <- .circle.SetLabelPositions(V2,radii=r,centres=centres)
+	V2 <- VennSetSetLabels(V2,SetLabels)
+	FaceLabels <- .default.FaceLabelPositions(V2)
+	V2 <- VennSetFaceLabels(V2,FaceLabels)
+
+	V2
 }
-setMethod("VisibleRange","CircleDrawing",function(object){
-	xymax <- object at centres+matrix(rep(object at radii,each=2),ncol=2,byrow=TRUE)
-	xymin <- object at centres-matrix(rep(object at radii,each=2),ncol=2,byrow=TRUE)
-	xy <- rbind(xymax,xymin); xy <- apply(xy,2,range)
-	xy
-}
-)
-setMethod("SetLabelPositions","CircleDrawing",function(object){
-	yscale <- diff(VisibleRange(object)[,2]); smidge <- 0.01*yscale
-	xy <- object at centres
-	xy[,2] <- xy[,2]+object at radii+smidge
+
+.circle.SetLabelPositions <- function(object,radii,centres){
+	yscale <- diff(VisibleRange(object)[,2]);
+	smidge <- 0.01*yscale
+	xy <- centres
+	abovebelow <- rep(1,NumberOfSets(object))
+	if (NumberOfSets(object)==3) {
+		abovebelow <- c(1,-1,-1)
+	}
+	xy[,2] <- xy[,2]+abovebelow*(radii+smidge)
 	VLabels <- data.frame(Label=rep("unset",nrow(xy)),x=NA,y=NA,hjust=I("center"),vjust=I("bottom"))
+	VLabels$vjust <- ifelse(abovebelow>0,"bottom","top")
 	VLabels[,2:3] <- xy
 	VLabels$Label <- VennSetNames(as(object,"Venn"))
 	VLabels
 }
-)
 
+
 # 2-d diagrams
 compute.C2 <- function(V,doWeights=TRUE,doEuler=FALSE) {
 	Vcalc <- V
@@ -59,6 +64,7 @@
 	r1 <- dList$r1;r2 <- dList$r2; d <- dList$d; 
 	C2 <- TwoCircles(r=c(r1,r2),d=d,V) # d in TwoCircles is distance of centre from origin
 	C2 <- .square.universe(C2,doWeights)
+	C2
 	
 }
 
@@ -191,9 +197,9 @@
 	} 
 	if (nodes>=10) stop("Still can't join circles")
 
-	C3 <- new("CircleDrawing",TM2,V,radii=r,centres=centres)
-	C3
-
+	C3 <- new("VennDrawing",TM2,V)
+	SetLabels <- .circle.SetLabelPositions(C3,radii=r,centres=centres)
+	C3 <- VennSetSetLabels(C3,SetLabels)
 }
 
 
@@ -281,6 +287,9 @@
 		C3 <- ThreeCircles(r=0.6,d=0.4,V=V)
 	}
 	C3 <- .square.universe(C3,doWeights=doWeights)
+	FaceLabels <- .default.FaceLabelPositions(C3)
+	C3 <- VennSetFaceLabels(C3,FaceLabels)
+
 	C3
 }
 

Modified: pkg/Vennerable/R/FourEllipses.R
===================================================================
--- pkg/Vennerable/R/FourEllipses.R	2009-09-18 17:14:09 UTC (rev 57)
+++ pkg/Vennerable/R/FourEllipses.R	2009-09-23 22:57:05 UTC (rev 58)
@@ -23,6 +23,10 @@
 	TM <- VennDiagrams[[type]][[n]]
 
 	VD <- new("VennDrawing",TM,V)
+	SetLabels <- .default.SetLabelPositions(VD)
+	VD <- VennSetSetLabels(VD,SetLabels)
+	FaceLabels <- .default.FaceLabelPositions(VD)
+	VD <- VennSetFaceLabels(VD,FaceLabels)
 	VD <- .square.universe(VD,doWeights)
 	VD
 

Modified: pkg/Vennerable/R/ThreeSquares.R
===================================================================
--- pkg/Vennerable/R/ThreeSquares.R	2009-09-18 17:14:09 UTC (rev 57)
+++ pkg/Vennerable/R/ThreeSquares.R	2009-09-23 22:57:05 UTC (rev 58)
@@ -1,13 +1,13 @@
 #warning("Entering ThreeSquares")
 
-setClass("SquareDrawing",representation("VennDrawing"))
-setMethod("SetLabelPositions","SquareDrawing",function(object) {
-	VLabel <- SetLabelPositions(as(object,"VennDrawing"))
-	if (nrow(VLabel)==2) {
-		VLabel[2,"hjust"] <- "right"
-	}
-	VLabel
-})
+#setClass("SquareDrawing",representation("VennDrawing"))
+#setMethod("SetLabelPositions","SquareDrawing",function(object) {
+##	VLabel <- SetLabelPositions(as(object,"VennDrawing"))
+#	if (nrow(VLabel)==2) {
+#		VLabel[2,"hjust"] <- "right"
+#	}
+#	VLabel
+#})
 	
 
 
@@ -64,8 +64,15 @@
 	TM <- addSetToDrawing (drawing1=VDP1 ,drawing2=VDP2, set2Name="Set2")
 	VD <- new("VennDrawing",TM,V)
 	VD <- .square.universe(VD,doWeights)
-	VS <- new("SquareDrawing",VD)
-	VS
+	SetLabels <- .default.SetLabelPositions(VD)
+	SetLabels[2,"hjust"] <- "right"
+	SetLabels[2,"x"] <- r2
+	VD <- VennSetSetLabels(VD,SetLabels)
+	FaceLabels <- .default.FaceLabelPositions(VD)
+	VD <- VennSetFaceLabels(VD,FaceLabels)
+
+#	VS <- new("SquareDrawing",VD)
+#	VS
 }
 
 
@@ -75,6 +82,9 @@
 	stopifnot(NumberOfSets(V)==3)
 	wght <- Weights(V)
 	VS <- VennSignature(V)
+	if ( doWeights & wght[VS=="111"]==0 ) {
+		stop("Can't generate a three squares plot for a nonzero central intersection")
+	}
 		
 	if (!doWeights) { 
 		x <- 1; y <- 3
@@ -97,6 +107,8 @@
 	
 	wac <- wght[VS=="101"] 
 	wac.height <- wac/wabc.width
+
+		
 	wac.x <- wabc.x
 	wac.y <-  wabc.height/2+c(0,0,wac.height,wac.height)
 	IntersectionShapes[["101"]] <- matrix(c(wac.x,wac.y),byrow=FALSE,ncol=2)
@@ -142,7 +154,9 @@
 		wb.y <- wabc.height/2-wb.height+c(0,0,wb.height,wb.height,wb.height-wbc.height,wb.height-wbc.height)
 	} else {
 	wb.width <- wab.width + wbc.width
-	if ( wb < wbc.width*(wab.height-wabc.height) ) {
+	wb.height <- wab.height
+	if ( wb < wbc.width*(wab.height-wabc.height) ) { # need to notch 010
+		# not sure this code has ever been tested, and last time I checked xa should be 1!
 		xa <- 2; xb <- wab.width + wbc.width +wab.height; xc <- - wb
 		db <- (-xb+sqrt(xb^2-4*xa*xc))/(2*xa)
 		wb.width <- wb.width+db
@@ -219,8 +233,12 @@
 	TM <- addSetToDrawing (drawing1=TM ,drawing2=VDP3, set2Name="Set3")
 	VD <- new("VennDrawing",TM,V)
 	VD <- .square.universe(VD,doWeights)
-	VS <- new("SquareDrawing",VD)
-	VS
+	SetLabels <- .default.SetLabelPositions(VD)
+	VD <- VennSetSetLabels(VD,SetLabels)
+	FaceLabels <- .default.FaceLabelPositions(VD)
+	VD <- VennSetFaceLabels(VD,FaceLabels)
+
+	VD
 }
 
 
@@ -281,6 +299,17 @@
 		TM <- addSetToDrawing(TM,Set[[ix]],set2Name=paste("Set",ix,sep=""))
 	}
 	VD <- new("VennDrawing",TM,V)
+	SetLabels <- .default.SetLabelPositions(VD)
+	VD <- VennSetSetLabels(VD,SetLabels)
+	FaceLabels <- .default.FaceLabelPositions(VD)
+	if (s>0) { # want the coordinates of face midpoints if s=0
+		Vtemp <- compute.S4(V,doWeights=FALSE,s=0,likeSquares=likeSquares)
+		FaceLabels <- VennGetFaceLabels(Vtemp)
+	} else { 
+		FaceLabels <- .default.FaceLabelPositions(VD)
+	}
+	VD <- VennSetFaceLabels(VD,FaceLabels)
+
 	VD <- .square.universe(VD,doWeights)
 
 

Modified: pkg/Vennerable/R/Triangles.R
===================================================================
--- pkg/Vennerable/R/Triangles.R	2009-09-18 17:14:09 UTC (rev 57)
+++ pkg/Vennerable/R/Triangles.R	2009-09-23 22:57:05 UTC (rev 58)
@@ -151,9 +151,14 @@
 	TM <- addSetToDrawing (drawing1=VDP1 ,drawing2=VDP2, set2Name="Set2")
 	TM <- addSetToDrawing (drawing1=TM ,drawing2=VDP3, set2Name="Set3")
 	VD <- new("VennDrawing",TM,Vorig)
+	SetLabels <- .default.SetLabelPositions(VD)
+	VD <- VennSetSetLabels(VD,SetLabels)
+	FaceLabels <- .default.FaceLabelPositions(VD)
+	VD <- VennSetFaceLabels(VD,FaceLabels)
 	VD <- .square.universe(VD,doWeights)
 
 
+
 }
 
 

Modified: pkg/Vennerable/inst/doc/TissueDrawingTest.Rnw
===================================================================
--- pkg/Vennerable/inst/doc/TissueDrawingTest.Rnw	2009-09-18 17:14:09 UTC (rev 57)
+++ pkg/Vennerable/inst/doc/TissueDrawingTest.Rnw	2009-09-23 22:57:05 UTC (rev 58)
@@ -1302,8 +1302,6 @@
 PlotSetBoundaries(Tstem)
 PlotNodes(Tstem)
 .validateDrawing(Tstem)
-try(IntersectionMidpoints(Tstem))
-
 @
 \caption{Chow-Ruskey weighted 4-set diagram with smudge warnings}
 \end{center}
@@ -1315,7 +1313,7 @@
 \hline
 Author & Jonathan Swinton
 \\
-CVS id of this document & ${}$Id${}$.
+SVN id of this document & ${}$Id${}$.
 \\
 Generated on & \today
 \\

Modified: pkg/Vennerable/inst/doc/TissueDrawingTest.pdf
===================================================================
--- pkg/Vennerable/inst/doc/TissueDrawingTest.pdf	2009-09-18 17:14:09 UTC (rev 57)
+++ pkg/Vennerable/inst/doc/TissueDrawingTest.pdf	2009-09-23 22:57:05 UTC (rev 58)
@@ -163,337 +163,80 @@
 (Ellipses)
 endobj
 113 0 obj
-<< /S /GoTo /D (section.18) >>
+<< /S /GoTo /D [114 0 R  /Fit ] >>
 endobj
-116 0 obj
-(Chow Ruskey)
-endobj
-117 0 obj
-<< /S /GoTo /D (subsection.18.1) >>
-endobj
-120 0 obj
-(Bug 522)
-endobj
-121 0 obj
-<< /S /GoTo /D (section.19) >>
-endobj
-124 0 obj
-(This document)
-endobj
-125 0 obj
-<< /S /GoTo /D [126 0 R  /Fit ] >>
-endobj
-153 0 obj <<
-/Length 897       
+116 0 obj <<
+/Length 267       
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/vennerable -r 58