[Vennerable-commits] r19 - in pkg/Vennerable: R inst/doc man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jul 28 09:03:08 CEST 2009
Author: js229
Date: 2009-07-28 09:03:08 +0200 (Tue, 28 Jul 2009)
New Revision: 19
Modified:
pkg/Vennerable/R/03VennDrawing.R
pkg/Vennerable/inst/doc/Venn.Rnw
pkg/Vennerable/man/VennThemes.Rd
Log:
Modified: pkg/Vennerable/R/03VennDrawing.R
===================================================================
--- pkg/Vennerable/R/03VennDrawing.R 2009-07-23 10:44:56 UTC (rev 18)
+++ pkg/Vennerable/R/03VennDrawing.R 2009-07-28 07:03:08 UTC (rev 19)
@@ -174,7 +174,7 @@
fillcols <- rep(fillcols,times=1+nSets/length(fillcols))
}
setcolours <-fillcols[1:nSets]; names(setcolours) <- names(drawing at setList)
- gp <- lapply(names(setcolours ),function(x)gpar(col=setcolours [[x]],fill=NA,lty=1));
+ gp <- lapply(names(setcolours ),function(x)gpar(col=setcolours [[x]],fill=NA,lty=1,lwd=3));
names(gp) <- names(setcolours)
gp
}
Modified: pkg/Vennerable/inst/doc/Venn.Rnw
===================================================================
--- pkg/Vennerable/inst/doc/Venn.Rnw 2009-07-23 10:44:56 UTC (rev 18)
+++ pkg/Vennerable/inst/doc/Venn.Rnw 2009-07-28 07:03:08 UTC (rev 19)
@@ -5,7 +5,6 @@
<<defmakeme,echo=FALSE,eval=FALSE>>=
makeme <- function() {
- if ("package:Vennerable" %in% search())detach("package:Vennerable")
library(weaver)
setwd("C:/JonathanSwinton/Vennerable/pkg/Vennerable/inst/doc")
Sweave(driver="weaver","Venn.Rnw",stylepath=FALSE,use.cache=FALSE)
@@ -22,7 +21,7 @@
\title{
-Venn diagrams in R with the \texttt{Vennerable} package
+Venn diagrams in R\\with the \texttt{Vennerable} package
}
\author{Jonathan Swinton\\\texttt{jonathan at swintons.net}}
@@ -41,34 +40,13 @@
<<loadstuff>>=
#library(Vennerable)
<<doremove,echo=FALSE>>=
+if ("package:Vennerable" %in% search())detach("package:Vennerable")
remove(list=setdiff(ls(),"makeme"));
library(Vennerable)
@
-<<loadfromsource,eval=FALSE>>=
-library(grid);library(lattice);library(graph);library(RBGL);library(reshape)
-library(RColorBrewer)
-source("../../R/00Venn.R")
-source("../../R/02TissueDrawing.R")
-source("../../R/03VennDrawing.R")
-source("../../R/Circles.R")
-source("../../R/ThreeSquares.R")
-source("../../R/Triangles.R")
-source("../../R/FourEllipses.R")
-source("../../R/AWFE.R")
-source("../../R/ChowRuskey.R")
-source("../../R/GraphTheory.R")
-@
<<defmakevp>>=
options(width=80)
-
-makevp.eqsc <- function(xrange,yrange) {
- # cf Fig 7.4 of Murrell R Graphics
- pushViewport(plotViewport(name="Vennmar",c(1,1,1,1)))
- pushViewport(viewport(name="Vennlay",layout=grid.layout(1,1,widths=diff(xrange),heights=diff(yrange),respect=TRUE)))
- pushViewport(viewport(name="Vennvp",layout.pos.row=1,layout.pos.col=1,xscale=xrange,yscale=yrange))
- }
-
@
\begin{center}
<<front,fig=TRUE,cache=TRUE,eval=TRUE>>=
@@ -105,7 +83,7 @@
Vstem
@
Although Vennerable can cope with 4-set Venn diagrams, for now we reduce to a three-set object
-<<to3>>=
+<<to3,echo=TRUE>>=
Vstem3 <- Vstem[,c("OCT4","SOX2","NANOG")]
Vstem3
@
@@ -435,7 +413,7 @@
<<S4figdef,echo=FALSE>>=
-showe <- list(SetLabels=FALSE,Faces=TRUE,FaceText="elements")
+showe <- list(SetLabels=FALSE,Faces=TRUE,FaceText="signature")
dosans <- function(V4,s,likeSquares) {
S4 <- compute.S4(V4,s=s,likeSquares=likeSquares)
gp <- gpSquare(S4)
@@ -548,12 +526,11 @@
\section{Weighted Venn diagrams}
There are repeated requests to generate Venn diagrams in which the areas of the faces
themselves are meant to carry information, mainly by being proportional to the intersection weights.
-Even when these diagrams can be drawn, they are not often a success in clearly displaying information. But we shall try any way.
-In general, these will be produced with the \texttt{doWeights=TRUE} argument.
+Even when these diagrams can be drawn,
+they are not often a success in their information-bearing mission. But we can try anyway, through use
+of the argument \texttt{doWeights=TRUE}. First of all we consider the case when all the visible intersection weights are nonzero.
-First of all we consider the case when all the visible intersection weights are nonzero.
-
\subsection{Weighted 2-set Venn diagrams for 2 Sets}
\subsubsection{Circles}
It is always possible to get an exactly area-weighted solution for two circles
@@ -943,6 +920,11 @@
\end{tabular}
\bibliographystyle{plain}
+
+<<echo=FALSE,results=tex,eval=FALSE>>=
+bib <- system.file( "doc", "Venn.bib", package = "Vennerable" )
+cat( "\\bibliography{",bib,"}\n",sep='')
+@
%\bibliography{Venn}
\end{document}
Modified: pkg/Vennerable/man/VennThemes.Rd
===================================================================
--- pkg/Vennerable/man/VennThemes.Rd 2009-07-23 10:44:56 UTC (rev 18)
+++ pkg/Vennerable/man/VennThemes.Rd 2009-07-28 07:03:08 UTC (rev 19)
@@ -21,7 +21,7 @@
}
}
\details{
-Set boundary colours are taken from the \code{\link{RColorBrewer}} \code{Set1} palette.
+Set boundary colours are taken from the \code{\link[RColorBrewer]{RColorBrewer}} \code{Set1} palette.
If \code{colourAlgorithm="signature"}, face fill colours are taken frome the \code{RColorBrewer} \code{YlOrRed}
palette based on the number of sets represented in the face, so eg all the faces corresponding to membership of a single set are pale yellow while the face corresponding to all the intersections is dark red.
If \code{colourAlgorithm="binary"}, faces are blue if they correspond to an odd number of intersections and white otherwise.
@@ -35,7 +35,6 @@
}
\value{
A list with four elements
-
\item{Face }{Named list of graphical parameters which will be applied to faces with corresponding names }
\item{FaceText }{Named list of graphical parameters which will be applied to annotation in faces with corresponding names }
\item{Set }{Named list of graphical parameters which will be applied to sets with corresponding names }
@@ -45,7 +44,7 @@
Jonathan Swinton (jonathan at swintons.net)
}
\seealso{
-See also \code{\link{RColorBrewer}}
+See also \code{\link[RColorBrewer]{RColorBrewer}}
}
\examples{
# change SetNames to large red text
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