[R-gregmisc-users] SF.net SVN: r-gregmisc:[1942] trunk/gplots

[<wa...@us...>]

Revision: 1942
          http://sourceforge.net/p/r-gregmisc/code/1942
Author:   warnes
Date:     2015-04-23 19:58:44 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
- The returned object from venn() now includes a 'interesection'
  attribution containing a list of which items are in each set
  intersection.  This can be turned off by settting
  'intersection=FALSE'.

Modified Paths:
--------------
    trunk/gplots/R/venn.R
    trunk/gplots/man/venn.Rd

Modified: trunk/gplots/R/venn.R
===================================================================
--- trunk/gplots/R/venn.R	2015-04-23 19:09:17 UTC (rev 1941)
+++ trunk/gplots/R/venn.R	2015-04-23 19:58:44 UTC (rev 1942)
@@ -1,7 +1,7 @@
 # This code plots Venn Diagrams for up to 5 sets. The
 # function getVennCounts is passed a list of vectors.
 # This is transformed into a table indicating the
-# number of members for each intersection. This table
+# number of intersections for each intersection. This table
 # is generated for any number of sets.
 
 # The function drawVennDiagram plots circles (up to three
@@ -23,16 +23,19 @@
       stop("Only indicator columns permitted")
 
     l <- lapply( l, function(x) which(as.logical(x)))
-    getVennCounts.list(l)
+    getVennCounts.list(l, universe=universe, verbose=verbose)
   }
 
 # l offers a list of arrays, their values are to
 # be tested for the size of their intersects.
-getVennCounts.list<-function(l, universe=NA, verbose=F) {
+getVennCounts.list<-function(l, universe=NA, verbose=F, intersections=TRUE) {
 	if (verbose) cat("Interpreting data as list.\n")
 	numSets<-length(l)
 	result.table<-NULL
 	result.table.names<-NULL
+
+	memberList <- list()
+
 	# Iteration over all possible intersections involving all sets
 	# or the complement (negation) of those sets.
 	for (i in 0:(-1 + 2^numSets)) {
@@ -104,8 +107,12 @@
 			sel<-NULL
 		}
 
+		r.name<-paste(i2,collapse="")
+		if (intersections) {
+			memberList[[r.name]] <- sel
+		}
+
 		r<-length(sel)
-		r.name<-paste(i2,collapse="")
 		result.row<-c(r,i2)
 		dim(result.row)<-c(1,length(result.row))
 		rownames(result.row)<-c(r.name)
@@ -132,6 +139,9 @@
 	else{
 		colnames(result.table)<-c("num",names(l))
 	}
+	if (intersections) {
+            attr(result.table,"intersections") <- memberList
+	}
         class(result.table) <- "venn"
 	return(result.table)
 }
@@ -144,9 +154,10 @@
                  small=0.7,
                  showSetLogicLabel=FALSE,
                  simplify=FALSE,
-                 show.plot=TRUE)
+                 show.plot=TRUE,
+                 intersections=TRUE)
 {
-  counts <- getVennCounts(data, universe=universe)
+  counts <- getVennCounts(data, universe=universe, intersections=intersections)
   
   if(show.plot)
     drawVennDiagram(data=counts,

Modified: trunk/gplots/man/venn.Rd
===================================================================
--- trunk/gplots/man/venn.Rd	2015-04-23 19:09:17 UTC (rev 1941)
+++ trunk/gplots/man/venn.Rd	2015-04-23 19:58:44 UTC (rev 1942)
@@ -7,14 +7,14 @@
 }
 \usage{
 venn(data, universe=NA, small=0.7, showSetLogicLabel=FALSE,
-     simplify=FALSE, show.plot=TRUE)
+     simplify=FALSE, show.plot=TRUE, intersections=TRUE)
 \method{plot}{venn}(x, y, ..., small=0.7, showSetLogicLabel=FALSE,
           simplify=FALSE)
 }
 \arguments{
   \item{data,x}{Either a list list containing vectors of names or indices
-    of group members, or a data frame containing boolean indicators of
-    group membership (see below)}
+    of group intersections, or a data frame containing boolean indicators of
+    group intersectionship (see below)}
   \item{universe}{Subset of valid name/index elements. Values  ignore values
     in code{data} not in this list will be ignored. Use \code{NA} to
     use all elements of \code{data} (the default).}
@@ -25,13 +25,17 @@
     should be omitted.}
   \item{show.plot}{Logical flag indicating whether the plot should be
     displayed.  If false, simply returns the group count matrix.}
+  \item{intersections}{Logical flag indicating
+    if the returned object should have the attribute
+    "individuals.in.intersections" featuring for every set a list of
+    individuals that are assigned to it.}
   \item{y,...}{Ignored}
 }
 \details{
   \code{data} should be either a named list of vectors containing
   character string names ("GeneAABBB", "GeneBBBCY", .., "GeneXXZZ") or
-  indexes of group members (1, 2, .., N), or a data frame containing
-  indicator variables (TRUE, FALSE, TRUE, ..) for group membership.
+  indexes of group intersections (1, 2, .., N), or a data frame containing
+  indicator variables (TRUE, FALSE, TRUE, ..) for group intersectionship.
   Group names will be taken from the component list element or column
   names.  
 }
@@ -39,7 +43,7 @@
   Invisibly returns an object of class "venn", containing a matrix of
   all possible sets of groups, and the observed count of items belonging
   to each The fist column contains observed counts, subsequent columns
-  contain 0-1 indicators of group membership.
+  contain 0-1 indicators of group intersectionship.
 }
 \author{
   Steffen Moeller \email{steffen\_mo...@gm...},
@@ -64,9 +68,9 @@
 input  <-list(GroupA,GroupB,GroupC,GroupD)
 input
 
-venn(input)
+tmp <- venn(input)
+attr(tmp, "intersections")
 
-
 ##
 ## Example using a list of item indexes belonging to the
 ## specified group.
@@ -131,6 +135,14 @@
 test <- function(x) (x \%in\% GroupA) & (x \%in\% GroupB) & !(x \%in\% GroupC)
 universe[ test(universe) ]
 
+##
+## Intriduced with gplots 2.16, the names of individuals for everz intersection
+## is offered as an attribute to the retrun value.
+##
 
+a<-venn(list(1:5,3:8),show.plot=F,intersections=TRUE)
+intersections<-attr(a,"intersections")
+print(intersections)
+
 }
 \keyword{hplot}

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