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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1826] trunk/SASxport/man/SASformat.Rd

From: <wa...@us...> - 2014-07-17 02:14:30

Revision: 1826
          http://sourceforge.net/p/r-gregmisc/code/1826
Author:   warnes
Date:     2014-07-17 02:14:21 +0000 (Thu, 17 Jul 2014)
Log Message:
-----------
Rename former 'label.Rd' file to 'SASformatRd' and remove references
to label() and "label<-"() (checkin missed from previous release).

Added Paths:
-----------
    trunk/SASxport/man/SASformat.Rd

Added: trunk/SASxport/man/SASformat.Rd
===================================================================
--- trunk/SASxport/man/SASformat.Rd	                        (rev 0)
+++ trunk/SASxport/man/SASformat.Rd	2014-07-17 02:14:21 UTC (rev 1826)
@@ -0,0 +1,91 @@
+\name{SASformat}
+
+\alias{SASformat}
+\alias{SASformat.default}
+\alias{SASformat<-}
+\alias{SASformat<-.default}
+
+\alias{SASiformat}
+\alias{SASiformat.default}
+\alias{SASiformat<-}
+\alias{SASiformat<-.default}
+
+\alias{SAStype}
+\alias{SAStype.default}
+\alias{SAStype<-}
+\alias{SAStype<-.default}
+
+\title{
+Set or Retreive the 'label', 'SASformat', 'SASiformat', or 'SAStype'
+attribute of a vector or (components of) a data frame
+}
+\description{
+  Sets or retrieves the %\code{"label"},%
+  \code{"SASformat"},
+  \code{"SASiformat"}, or \code{SAStype} attribute of an object.
+
+  More comprehensive support for object labels, and SASformat, are
+  available in Frank Harrell's \code{Hmisc} package.
+
+  Note that \code{SAStype} enforces the SAS 8-character naming convention.
+}
+\usage{
+SASformat(x, default)
+SASformat(x) <- value
+
+SASiformat(x, default)
+SASiformat(x) <- value
+
+SAStype(x, default)
+SAStype(x) <- value
+}
+\arguments{
+\item{x}{any object}
+\item{value}{new value for the  \code{"label"}, \code{"SASformat"},
+  \code{"SASiformat"}, or \code{SAStype}  attribute of an object.}
+\item{default}{value to return when no appropriate attribute is
+  found.  The usual return value is NULL.}
+}
+\value{
+  the contents of the \code{"label"}, \code{"SASformat"},
+  \code{"SASiformat"}, \code{"SAStype"} attribute of x, if any;
+  otherwise, the value provided by \code{default}.
+}
+\author{
+  Gregory R. Warnes \email{gr...@wa...} based on code from the
+  \code{Hmisc} library by Frank E. Harrell, Jr.  ]
+}
+%\seealso{
+%}
+\examples{
+
+## Examples for vectors
+
+fail.time <- c(10,20)
+
+# set attributes
+%% label(fail.time) <- 'Failure Time'
+SASformat(fail.time) <- 'Numeric2'
+SASiformat(fail.time) <- 'Numeric2'
+
+# display individual attributes
+%% label(fail.time)
+SASformat(fail.time)
+SASiformat(fail.time)
+
+# display all attributes
+attributes(fail.time)
+
+## SAStype only applies to data frames
+df <- data.frame( fail.time, day=c("Mon","Tue") )
+SAStype(df) <- "USER"
+
+SAStype(df)
+
+## Example showing specification of default return value
+a <- 70
+label(a, default="no label")
+}
+\keyword{utilities}
+\keyword{interface}
+

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1825] trunk/SASxport/R/read.xport.R

From: <wa...@us...> - 2014-07-17 00:27:38

Revision: 1825
          http://sourceforge.net/p/r-gregmisc/code/1825
Author:   warnes
Date:     2014-07-17 00:27:29 +0000 (Thu, 17 Jul 2014)
Log Message:
-----------
read.xport: Preserve '$' at the beginning of SAS character format strings.

Modified Paths:
--------------
    trunk/SASxport/R/read.xport.R

Modified: trunk/SASxport/R/read.xport.R
===================================================================
--- trunk/SASxport/R/read.xport.R	2014-07-17 00:14:58 UTC (rev 1824)
+++ trunk/SASxport/R/read.xport.R	2014-07-17 00:27:29 UTC (rev 1825)
@@ -130,10 +130,10 @@
       names(w) <- nam
       dinfo    <- dsinfo[[k]]
 
-      fmt      <- sub('^\\$','',dinfo$format)
+      fmt <- dinfo$format
       formats  <- fstr( fmt, dinfo$flength, dinfo$fdigits)
 
-      ifmt     <- sub('^\\$','',dinfo$iformat)
+      ifmt <- dinfo$iformat
       iformats <- fstr( ifmt, dinfo$iflength, dinfo$ifdigits)
 
       lab      <- dinfo$label

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1824] trunk/SASxport/R/read.xport.R

From: <wa...@us...> - 2014-07-17 00:15:02

Revision: 1824
          http://sourceforge.net/p/r-gregmisc/code/1824
Author:   warnes
Date:     2014-07-17 00:14:58 +0000 (Thu, 17 Jul 2014)
Log Message:
-----------
read.xport() argument names.tolower was not being honored for dataset
names.

Modified Paths:
--------------
    trunk/SASxport/R/read.xport.R

Modified: trunk/SASxport/R/read.xport.R
===================================================================
--- trunk/SASxport/R/read.xport.R	2014-06-30 19:26:21 UTC (rev 1823)
+++ trunk/SASxport/R/read.xport.R	2014-07-17 00:14:58 UTC (rev 1824)
@@ -102,7 +102,7 @@
     else
       names.tolower <- function(x) x
 
-    dsn <- tolower(which.regular)
+    dsn <- names.tolower(which.regular)
 
     res <- vector('list', nds)
     names(res) <- gsub('_','.',dsn)

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1823] trunk/gplots/R/heatmap.2.R

From: <wa...@us...> - 2014-06-30 19:26:24

Revision: 1823
          http://sourceforge.net/p/r-gregmisc/code/1823
Author:   warnes
Date:     2014-06-30 19:26:21 +0000 (Mon, 30 Jun 2014)
Log Message:
-----------
Fix typo in dendrogram size checking code.

Modified Paths:
--------------
    trunk/gplots/R/heatmap.2.R

Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R	2014-06-19 18:51:32 UTC (rev 1822)
+++ trunk/gplots/R/heatmap.2.R	2014-06-30 19:26:21 UTC (rev 1823)
@@ -210,7 +210,7 @@
     {
       ddc <- Colv ## use Colv 'as-is', when it is dendrogram
       colInd <- order.dendrogram(ddc)
-      if(length(colInd)>nr || any(colInd<1 | colInd > nc ))
+      if(length(colInd)>nc || any(colInd<1 | colInd > nc ))
          stop("Colv dendrogram doesn't match size of x")
     }
   else if(identical(Colv, "Rowv")) {

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1822] trunk/gplots/R/heatmap.2.R

From: <wa...@us...> - 2014-06-19 18:51:40

Revision: 1822
          http://sourceforge.net/p/r-gregmisc/code/1822
Author:   warnes
Date:     2014-06-19 18:51:32 +0000 (Thu, 19 Jun 2014)
Log Message:
-----------
Fix typo 'ColInd' --> 'colInd'.

Modified Paths:
--------------
    trunk/gplots/R/heatmap.2.R

Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R	2014-06-19 18:36:19 UTC (rev 1821)
+++ trunk/gplots/R/heatmap.2.R	2014-06-19 18:51:32 UTC (rev 1822)
@@ -210,7 +210,7 @@
     {
       ddc <- Colv ## use Colv 'as-is', when it is dendrogram
       colInd <- order.dendrogram(ddc)
-      if(length(ColInd)>nr || any(colInd<1 | colInd > nc ))
+      if(length(colInd)>nr || any(colInd<1 | colInd > nc ))
          stop("Colv dendrogram doesn't match size of x")
     }
   else if(identical(Colv, "Rowv")) {

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1821] trunk/gplots

From: <wa...@us...> - 2014-06-19 18:36:29

Revision: 1821
          http://sourceforge.net/p/r-gregmisc/code/1821
Author:   warnes
Date:     2014-06-19 18:36:19 +0000 (Thu, 19 Jun 2014)
Log Message:
-----------
Update for gplots 2.14.0

Modified Paths:
--------------
    trunk/gplots/DESCRIPTION
    trunk/gplots/inst/NEWS

Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION	2014-06-17 23:22:57 UTC (rev 1820)
+++ trunk/gplots/DESCRIPTION	2014-06-19 18:36:19 UTC (rev 1821)
@@ -4,8 +4,8 @@
 Depends: R (>= 3.0)
 Imports: gtools, gdata, stats, caTools, KernSmooth
 Suggests: grid, MASS
-Version: 2.13.0
-Date: 2014-04-04
+Version: 2.14.0
+Date: 2014-06-19
 Author: Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert
 	Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin
 	Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz, Bill

Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS	2014-06-17 23:22:57 UTC (rev 1820)
+++ trunk/gplots/inst/NEWS	2014-06-19 18:36:19 UTC (rev 1821)
@@ -1,3 +1,27 @@
+Release 2.14.0 - 2014-06-18
+---------------------------
+
+Bug Fixes:
+
+- heatmap.2(): Fix typo in heatmap.2() that caused an error when
+  'Rowv=FALSE'. (Reported by Yuanhua Liu.)
+
+Enhancements:
+
+- heatmap.2(): Add new 'reorderfun' argument to allow the user to
+  specify an alternative function to reorder rows/columns based on
+  row/column dendrogram. (Suggested by Yuanhua Liu.)
+
+- heatmap.2(): Center margin labels.
+
+- heatmap.2(): Check size of user-provided Rowv and Colv dendrogram
+  objects to ensure they match the dimensions of the data.
+
+- Add references to man page for hist2d() and ci2d() to the new r2d2
+  package which implements an improved algorithm for 2-dimensional
+  emprical confidence regions.
+
+
 Release 2.13.0 - 2014-04-04
 ---------------------------
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1820] trunk/gplots/man/heatmap.2.Rd

From: <wa...@us...> - 2014-06-17 23:23:01

Revision: 1820
          http://sourceforge.net/p/r-gregmisc/code/1820
Author:   warnes
Date:     2014-06-17 23:22:57 +0000 (Tue, 17 Jun 2014)
Log Message:
-----------
- Document new 'key.title', 'key.xlab', 'key.ylab', 'key.xtickfun',
  'key.ytickfun', 'key.par' arguments to heatmap.2 (belated commit).
- Document new 'reorderfun' argument to heatmap.2.

Modified Paths:
--------------
    trunk/gplots/man/heatmap.2.Rd

Modified: trunk/gplots/man/heatmap.2.Rd
===================================================================
--- trunk/gplots/man/heatmap.2.Rd	2014-06-17 23:19:46 UTC (rev 1819)
+++ trunk/gplots/man/heatmap.2.Rd	2014-06-17 23:22:57 UTC (rev 1820)
@@ -20,6 +20,7 @@
            distfun = dist,
            hclustfun = hclust,
            dendrogram = c("both","row","column","none"),
+           reorderfun = function(d, w) reorder(d, w),
            symm = FALSE,
 
            # data scaling
@@ -78,6 +79,12 @@
            denscol=tracecol,
            symkey = min(x < 0, na.rm=TRUE) || symbreaks,
            densadj = 0.25,
+           key.title = NULL,
+           key.xlab = NULL,
+           key.ylab = NULL,
+           key.xtickfun = NULL,
+           key.ytickfun = NULL,
+           key.par=list(),
 
            # plot labels
            main = NULL,
@@ -95,7 +102,7 @@
            )
            }
 \arguments{
-  % Dendogram Control
+  % Dendrogram Control
   \item{x}{numeric matrix of the values to be plotted. }
   \item{Rowv}{determines if and how the \emph{row} dendrogram should be
     reordered.	By default, it is TRUE, which implies dendrogram is
@@ -115,15 +122,17 @@
     \code{\link{hclust}}.}
   \item{dendrogram}{character string indicating whether to draw 'none',
     'row', 'column' or 'both' dendrograms.  Defaults to 'both'. However,
-  if Rowv (or Colv) is FALSE or NULL and dendrogram is 'both', then a
-  warning is issued and Rowv (or Colv) arguments are honoured.}
+    if Rowv (or Colv) is FALSE or NULL and dendrogram is 'both', then a
+    warning is issued and Rowv (or Colv) arguments are honoured.}
+  \item{reorderfun}{\code{function(d, w)} of dendrogram and weights for
+    reordering the row and column dendrograms.  The default uses
+    \code{\link{stats}{reorder.dendrogram}}.
   \item{symm}{logical indicating if \code{x} should be treated
     \bold{symm}etrically; can only be true when \code{x} is a square matrix.}
   % data scaling
   \item{scale}{character indicating if the values should be centered and
     scaled in either the row direction or the column direction, or
-    none.  The default is \code{"row"} if \code{symm} false, and
-    \code{"none"} otherwise.}
+    none.  The default is \code{"none"}.}
   \item{na.rm}{logical indicating whether \code{NA}'s should be removed.}
   % image plot
   \item{revC}{logical indicating if the column order should be
@@ -207,6 +216,20 @@
     a density plot is drawn on the color key.  (See the \code{adjust}
     parameter for the \code{density} function for details.)  Defaults to
     0.25.}
+  \item{key.title}{main title of the color key. If set to NA no title
+    will be plotted.}
+  \item{key.xlab}{x axis label of the color key. If set to NA no label
+    will be plotted.}
+  \item{key.ylab}{y axis label of the color key. If set to NA no label
+    will be plotted.}
+  \item{key.xtickfun}{function computing tick location and labels for
+    the xaxis of the color key. Returns a named list containing
+    parameters that can be passed to \code{axis}. See examples.}
+  \item{key.ytickfun}{function computing tick location and labels for
+      the y axis of the color key. Returns a named list containing
+      parameters that can be passed to \code{axis}.  See examples.}
+  \item{key.par}{graphical parameters for the color key. Named list that
+    can be passed to \code{par}.}
   % plot labels
   \item{main, xlab, ylab}{main, x- and y-axis titles; defaults to none.}
   % figure layout
@@ -234,19 +257,19 @@
   If either is \code{\link{NULL}}, \emph{no reordering} will be done for
   the corresponding side.
 
-  If \code{scale="row"} the rows are scaled to have mean
-  zero and standard deviation one.  There is some empirical evidence
-  from genomic plotting that this is useful.
+  If \code{scale="row"} (or \code{scale="col"}) the rows (columns) are
+  scaled to have mean zero and standard deviation one.  There is some
+  empirical evidence from genomic plotting that this is useful.
 
   The default colors range from red to white (\code{heat.colors}) and
-  are not pretty.  Consider using enhancements such
-  as the \pkg{RColorBrewer} package,
+  are not pretty.  Consider using enhancements such as the
+  \pkg{RColorBrewer} package,
   \url{http://cran.r-project.org/src/contrib/PACKAGES.html#RColorBrewer}
   to select better colors.
 
   By default four components will be displayed in the plot.  At the top
-  left is the color key, top right is the column dendogram, bottom left
-  is the row dendogram, bottom right is the image plot.  When
+  left is the color key, top right is the column dendrogram, bottom left
+  is the row dendrogram, bottom right is the image plot.  When
   RowSideColor or ColSideColor are provided, an additional row or column
   is inserted in the appropriate location.   This layout can be
   overriden by specifiying appropriate values for \code{lmat},
@@ -257,16 +280,13 @@
   arguments.
 }
 \note{
-  The original rows and columns are reordered \emph{in any case} to
-  match the dendrogram, e.g., the rows by
-  \code{\link{order.dendrogram}(Rowv)} where \code{Rowv} is the
-  (possibly \code{\link{reorder}()}ed) row dendrogram.
+  The original rows and columns are reordered to match the dendrograms
+  \code{Rowv} and \code{Colv} (if present).
 
-  \code{heatmap.2()} uses \code{\link{layout}} and draws the
-  \code{\link{image}} in the lower right corner of a 2x2 layout.
-  Consequentially, it can \bold{not} be used in a multi column/row
-  layout, i.e., when \code{\link{par}(mfrow= *)} or \code{(mfcol= *)}
-  has been called.
+  \code{heatmap.2()} uses \code{\link{layout}} to arragent the plot
+  elements. Consequentially, it can \bold{not} be used in a multi
+  column/row layout using \code{\link{layout}(\dots)},
+  \code{\link{par}(mfrow=\dots)} or \code{(mfcol=\dots)}.
 }
 \value{
   Invisibly, a list with components
@@ -304,7 +324,7 @@
  cc <- rainbow(ncol(x), start=0, end=.3)
 
  ##
- ## demonstrate the effect of row and column dendogram options
+ ## demonstrate the effect of row and column dendrogram options
  ##
  heatmap.2(x)  ## default - dendrogram plotted and reordering done.
  heatmap.2(x, dendrogram="none") ##  no dendrogram plotted, but reordering done.
@@ -317,6 +337,10 @@
  heatmap.2(x, Rowv=NULL, dendrogram="both")  ## generate warning!
  heatmap.2(x, Colv=FALSE, dendrogram="both") ## generate warning!
 
+ ## Reorder dendrogram by branch means rather than sums
+ heatmap.2(x, reorderfun=function(d, w) reorder(d, w, agglo.FUN = mean) )
+
+
  ## Show effect of row and column label rotation
  heatmap.2(x, srtCol=NULL)
  heatmap.2(x, srtCol=0,   adjCol = c(0.5,1) )
@@ -332,6 +356,7 @@
  heatmap.2(x, srtRow=45, adjRow=c(0, 1), srtCol=45, adjCol=c(1,1) )
  heatmap.2(x, srtRow=45, adjRow=c(0, 1), srtCol=270, adjCol=c(0,0.5) )
 
+
  ## Show effect of offsetRow/offsetCol (only works when srtRow/srtCol is
  ## not also present)
  heatmap.2(x, offsetRow=0, offsetCol=0)
@@ -344,6 +369,7 @@
  heatmap.2(x, srtRow=0, srtCol=90, offsetRow=2, offsetCol=2)
  heatmap.2(x, srtRow=0, srtCol=90, offsetRow=-1, offsetCol=-1)
 
+
  ## Show how to use 'extrafun' to replace the 'key' with a scatterplot
  lmat <- rbind( c(5,3,4), c(2,1,4) )
  lhei <- c(1.5, 4)
@@ -357,7 +383,42 @@
 
  heatmap.2(x, lmat=lmat, lhei=lhei, lwid=lwid, key=FALSE, extrafun=myplot)
 
+ ## show how to customize the color key
+ heatmap.2(x,
+           key.title=NA, # no title
+           key.xlab=NA,  # no xlab
+           key.par=list(mgp=c(1.5, 0.5, 0),
+                        mar=c(2.5, 2.5, 1, 0)),
+           key.xtickfun=function() {
+                 breaks <- parent.frame()$breaks
+                 return(list(
+                      at=parent.frame()$scale01(c(breaks[1],
+                                                  breaks[length(breaks)])),
+                      labels=c(as.character(breaks[1]),
+                               as.character(breaks[length(breaks)]))
+                      ))
+           })
 
+ heatmap.2(x,
+          breaks=256,
+          key.title=NA,
+          key.xlab=NA,
+          key.par=list(mgp=c(1.5, 0.5, 0),
+                       mar=c(1, 2.5, 1, 0)),
+          key.xtickfun=function() {
+               cex <- par("cex")*par("cex.axis")
+               side <- 1
+               line <- 0
+               col <- par("col.axis")
+               font <- par("font.axis")
+               mtext("low", side=side, at=0, adj=0,
+                     line=line, cex=cex, col=col, font=font)
+               mtext("high", side=side, at=1, adj=1,
+                     line=line, cex=cex, col=col, font=font)
+               return(list(labels=FALSE, tick=FALSE))
+          })
+
+
  ##
  ## Show effect of z-score scaling within columns, blue-red color scale
  ##

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1819] trunk/gplots/R/heatmap.2.R

From: <wa...@us...> - 2014-06-17 23:19:50

Revision: 1819
          http://sourceforge.net/p/r-gregmisc/code/1819
Author:   warnes
Date:     2014-06-17 23:19:46 +0000 (Tue, 17 Jun 2014)
Log Message:
-----------
Allow user to specify function used to reorder based on the dendogram
via a new 'reorderfun' argument.  Suggested by Yuanhua Liu.

Modified Paths:
--------------
    trunk/gplots/R/heatmap.2.R

Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R	2014-06-17 20:34:17 UTC (rev 1818)
+++ trunk/gplots/R/heatmap.2.R	2014-06-17 23:19:46 UTC (rev 1819)
@@ -8,6 +8,7 @@
                        distfun = dist,
                        hclustfun = hclust,
                        dendrogram = c("both","row","column","none"),
+                       reorderfun = function(d, w) reorder(d, w),
                        symm = FALSE,
 
                        ## data scaling
@@ -109,13 +110,6 @@
             "specified can produce unpredictable results.",
             "Please consider using only one or the other.")
 
-  ## key & density don't make sense when data is not all on the same scale
-  ##    if(scale!="none" &&  key==TRUE)
-  ##      {
-  ##        warning("Key cannot be plotted when scale!=\"none\".")
-  ##        key=FALSE
-  ##      }
-
   if ( is.null(Rowv) || is.na(Rowv) )
     Rowv <- FALSE
   if ( is.null(Colv) || is.na(Colv) )
@@ -190,7 +184,7 @@
     { ## Compute dendrogram and do reordering based on given vector
       hcr <- hclustfun(distfun(x))
       ddr <- as.dendrogram(hcr)
-      ddr <-  reorder(ddr, Rowv)
+      ddr <-  reorderfun(ddr, Rowv)
 
       rowInd <- order.dendrogram(ddr)
       if(nr != length(rowInd))
@@ -201,7 +195,7 @@
       Rowv <- rowMeans(x, na.rm = na.rm)
       hcr <- hclustfun(distfun(x))
       ddr <- as.dendrogram(hcr)
-      ddr <- reorder(ddr, Rowv)
+      ddr <- reorderfun(ddr, Rowv)
 
       rowInd <- order.dendrogram(ddr)
       if(nr != length(rowInd))
@@ -232,7 +226,7 @@
     {## Compute dendrogram and do reordering based on given vector
       hcc <- hclustfun(distfun(if(symm)x else t(x)))
       ddc <- as.dendrogram(hcc)
-      ddc <- reorder(ddc, Colv)
+      ddc <- reorderfun(ddc, Colv)
 
       colInd <- order.dendrogram(ddc)
       if(nc != length(colInd))
@@ -243,7 +237,7 @@
       Colv <- colMeans(x, na.rm = na.rm)
       hcc <- hclustfun(distfun(if(symm)x else t(x)))
       ddc <- as.dendrogram(hcc)
-      ddc <- reorder(ddc, Colv)
+      ddc <- reorderfun(ddc, Colv)
 
       colInd <- order.dendrogram(ddc)
       if(nc != length(colInd))

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1818] trunk/gplots/R/heatmap.2.R

From: <wa...@us...> - 2014-06-17 20:34:24

Revision: 1818
          http://sourceforge.net/p/r-gregmisc/code/1818
Author:   warnes
Date:     2014-06-17 20:34:17 +0000 (Tue, 17 Jun 2014)
Log Message:
-----------
Fix typo in heatmap.2() reported by Yuanhua Liu.

Modified Paths:
--------------
    trunk/gplots/R/heatmap.2.R

Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R	2014-06-05 17:21:11 UTC (rev 1817)
+++ trunk/gplots/R/heatmap.2.R	2014-06-17 20:34:17 UTC (rev 1818)
@@ -147,7 +147,7 @@
         if (is.logical(Colv) && (Colv))
           dendrogram <- "column"
         else
-          dedrogram <- "none"
+          dendrogram <- "none"
 
         warning("Discrepancy: Rowv is FALSE, while dendrogram is `",
                 dendrogram, "'. Omitting row dendogram.")

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1817] trunk/gplots/R/heatmap.2.R

From: <wa...@us...> - 2014-06-05 17:21:17

Revision: 1817
          http://sourceforge.net/p/r-gregmisc/code/1817
Author:   warnes
Date:     2014-06-05 17:21:11 +0000 (Thu, 05 Jun 2014)
Log Message:
-----------
Check size of Rowv and Colv dendogram objects to ensure they matches data.

Modified Paths:
--------------
    trunk/gplots/R/heatmap.2.R

Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R	2014-05-28 00:24:23 UTC (rev 1816)
+++ trunk/gplots/R/heatmap.2.R	2014-06-05 17:21:11 UTC (rev 1817)
@@ -183,6 +183,8 @@
     {
       ddr <- Rowv ## use Rowv 'as-is', when it is dendrogram
       rowInd <- order.dendrogram(ddr)
+      if(length(rowInd)>nr || any(rowInd<1 | rowInd > nr ))
+         stop("Rowv dendrogram doesn't match size of x")
     }
   else if (is.integer(Rowv))
     { ## Compute dendrogram and do reordering based on given vector
@@ -214,6 +216,8 @@
     {
       ddc <- Colv ## use Colv 'as-is', when it is dendrogram
       colInd <- order.dendrogram(ddc)
+      if(length(ColInd)>nr || any(colInd<1 | colInd > nc ))
+         stop("Colv dendrogram doesn't match size of x")
     }
   else if(identical(Colv, "Rowv")) {
     if(nr != nc)

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1816] trunk/gtools

From: <wa...@us...> - 2014-05-28 00:24:27

Revision: 1816
          http://sourceforge.net/p/r-gregmisc/code/1816
Author:   warnes
Date:     2014-05-28 00:24:23 +0000 (Wed, 28 May 2014)
Log Message:
-----------
Update for gtools 3.4.1

Modified Paths:
--------------
    trunk/gtools/DESCRIPTION
    trunk/gtools/inst/NEWS

Modified: trunk/gtools/DESCRIPTION
===================================================================
--- trunk/gtools/DESCRIPTION	2014-05-28 00:18:38 UTC (rev 1815)
+++ trunk/gtools/DESCRIPTION	2014-05-28 00:24:23 UTC (rev 1816)
@@ -1,8 +1,8 @@
 Package: gtools
 Title: Various R programming tools
 Description: Various R programming tools
-Version: 3.4.0
-Date: 2014-04-15
+Version: 3.4.1
+Date: 2014-05-27
 Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
 Maintainer: Gregory R. Warnes <gr...@wa...>
 License: LGPL-2.1

Modified: trunk/gtools/inst/NEWS
===================================================================
--- trunk/gtools/inst/NEWS	2014-05-28 00:18:38 UTC (rev 1815)
+++ trunk/gtools/inst/NEWS	2014-05-28 00:24:23 UTC (rev 1816)
@@ -1,3 +1,17 @@
+gtools 3.4.1 - 2014-05-27
+-------------------------
+
+Bug fixes:
+
+- smartbind() now converts all non-atomic type columns (except factor)
+  to type character instead of generating an opaque error message.
+
+Other changes:
+
+- the argument to ASCIIfy() is now named 'x' instead of 'string'.
+
+- minor formatting changes to ASCIIfy() man page.
+
 gtools 3.4.0 - 2014-04-14
 -------------------------
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1815] trunk/gtools/tests/smartbind_Dates.R

From: <wa...@us...> - 2014-05-28 00:18:42

Revision: 1815
          http://sourceforge.net/p/r-gregmisc/code/1815
Author:   warnes
Date:     2014-05-28 00:18:38 +0000 (Wed, 28 May 2014)
Log Message:
-----------
Add test to ensure smartbind() properly handles Date columns.

Added Paths:
-----------
    trunk/gtools/tests/smartbind_Dates.R

Added: trunk/gtools/tests/smartbind_Dates.R
===================================================================
--- trunk/gtools/tests/smartbind_Dates.R	                        (rev 0)
+++ trunk/gtools/tests/smartbind_Dates.R	2014-05-28 00:18:38 UTC (rev 1815)
@@ -0,0 +1,9 @@
+library(gtools)
+
+today <- Sys.Date()
+tenweeks <- seq(today, length.out=10, by="1 week")
+
+df1 <- data.frame(dates=tenweeks, chars=letters[1:10], ints=1:10, numeric=1.1:10.1)
+df2 <- data.frame(chars=letters[11:20], ints=11:20, numeric=11.1:20.1)
+
+smartbind(df1, df2)

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1814] trunk/gtools/R/smartbind.R

From: <wa...@us...> - 2014-05-28 00:15:00

Revision: 1814
          http://sourceforge.net/p/r-gregmisc/code/1814
Author:   warnes
Date:     2014-05-28 00:14:56 +0000 (Wed, 28 May 2014)
Log Message:
-----------
smartbind: Convert non-native type columns (except factor) to character.

Modified Paths:
--------------
    trunk/gtools/R/smartbind.R

Modified: trunk/gtools/R/smartbind.R
===================================================================
--- trunk/gtools/R/smartbind.R	2014-04-18 18:11:20 UTC (rev 1813)
+++ trunk/gtools/R/smartbind.R	2014-05-28 00:14:56 UTC (rev 1814)
@@ -63,18 +63,33 @@
                                 "  End:", end,
                                 "  Column:", col,
                                 "\n", sep="")
+
                 if ("factor" %in% classVec)
                   {
                     newclass <- "character"
                   }
                 else
-                  newclass <- classVec
+                  newclass <- classVec[1]
 
+                ## Coerce everything that isn't a native type to character
+                if(! (newclass %in% c("logical", "integer", "numeric",
+                                     "complex", "character", "raw") ))
+                    {
+                        newclass <- "character"
+                        warning("Converting non-atomic type column '", col,
+                                "' to type character.")
+                    }
+
                 retval[[col]] <- as.vector(rep(fill,nrows), mode=newclass)
               }
 
-            retval[[col]][start:end] <- as.vector(block[,col],
-                                                  mode=class(retval[[col]]))
+            mode <- class(retval[[col]])
+            if(mode=="character")
+                vals <- as.character(block[,col])
+            else
+                vals <- block[,col]
+
+            retval[[col]][start:end] <- as.vector(vals, mode=mode)
           }
         start <- end+1
         blockIndex <- blockIndex+1

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1813] trunk/gtools

From: <ar...@us...> - 2014-04-18 18:11:23

Revision: 1813
          http://sourceforge.net/p/r-gregmisc/code/1813
Author:   arnima
Date:     2014-04-18 18:11:20 +0000 (Fri, 18 Apr 2014)
Log Message:
-----------
Main arg is 'x' like showNonASCII(x), preformatted notes instead of verb

Modified Paths:
--------------
    trunk/gtools/R/ASCIIfy.R
    trunk/gtools/man/ASCIIfy.Rd

Modified: trunk/gtools/R/ASCIIfy.R
===================================================================
--- trunk/gtools/R/ASCIIfy.R	2014-04-17 19:05:11 UTC (rev 1812)
+++ trunk/gtools/R/ASCIIfy.R	2014-04-18 18:11:20 UTC (rev 1813)
@@ -1,4 +1,4 @@
-ASCIIfy <- function(string, bytes=2, fallback="?")
+ASCIIfy <- function(x, bytes=2, fallback="?")
 {
   bytes <- match.arg(as.character(bytes), 1:2)
   convert <- function(char)  # convert to ASCII, e.g. "z", "\xfe", or "\u00fe"
@@ -23,13 +23,13 @@
     return(ascii)
   }
 
-  if(length(string) > 1)
+  if(length(x) > 1)
   {
-    sapply(string, ASCIIfy, bytes=bytes, fallback=fallback, USE.NAMES=FALSE)
+    sapply(x, ASCIIfy, bytes=bytes, fallback=fallback, USE.NAMES=FALSE)
   }
   else
   {
-    input <- unlist(strsplit(string,""))  # "c"  "a"  "f"  "<\'e>"
+    input <- unlist(strsplit(x,""))       # "c"  "a"  "f"  "<\'e>"
     output <- character(length(input))    # ""   ""   ""   ""
     for(i in seq_along(input))
       output[i] <- convert(input[i])      # "c"  "a"  "f"  "\\u00e9"

Modified: trunk/gtools/man/ASCIIfy.Rd
===================================================================
--- trunk/gtools/man/ASCIIfy.Rd	2014-04-17 19:05:11 UTC (rev 1812)
+++ trunk/gtools/man/ASCIIfy.Rd	2014-04-18 18:11:20 UTC (rev 1813)
@@ -6,10 +6,10 @@
   single-byte (\samp{\x00}) or two-byte (\samp{\u0000}) codes.
 }
 \usage{
-ASCIIfy(string, bytes = 2, fallback = "?")
+ASCIIfy(x, bytes = 2, fallback = "?")
 }
 \arguments{
-  \item{string}{a character vector, possibly containing non-ASCII
+  \item{x}{a character vector, possibly containing non-ASCII
     characters.}
   \item{bytes}{either \code{1} or \code{2}, for single-byte
     (\samp{\x00}) or two-byte (\samp{\u0000}) codes.}
@@ -23,7 +23,7 @@
 \author{Arni Magnusson \email{ar...@ha...}}
 \note{
   To render single backslashes, use these or similar techniques:
-  \verb{
+  \preformatted{
     write(ASCIIfy(x), "file.txt")
     cat(paste(ASCIIfy(x), collapse="\n"), "\n", sep="")}
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1812] trunk/gplots/man/hist2d.Rd

From: <wa...@us...> - 2014-04-17 19:05:15

Revision: 1812
          http://sourceforge.net/p/r-gregmisc/code/1812
Author:   warnes
Date:     2014-04-17 19:05:11 +0000 (Thu, 17 Apr 2014)
Log Message:
-----------
Add see also to r2d2::freq2d.

Modified Paths:
--------------
    trunk/gplots/man/hist2d.Rd

Modified: trunk/gplots/man/hist2d.Rd
===================================================================
--- trunk/gplots/man/hist2d.Rd	2014-04-17 19:03:08 UTC (rev 1811)
+++ trunk/gplots/man/hist2d.Rd	2014-04-17 19:05:11 UTC (rev 1812)
@@ -39,7 +39,6 @@
   then constucted which holds the counts of the number of observed (x,y) pairs
   that fall into each bin.  If \code{show=TRUE}, this matrix is then
   then passed to \code{image} for display.
-
 }
 \value{
   A list containing 5 elements:
@@ -50,7 +49,10 @@
   }
 \author{ Gregory R. Warnes \email{gr...@wa...}}
 
-\seealso{ \code{\link{image}}, \code{\link{persp}}, \code{\link{hist}} }
+\seealso{
+  \code{\link{image}}, \code{\link{persp}}, \code{\link{hist}},
+  \code{\link[r2d2]{freq2d}} 
+  }
 
 \examples{
    ## example data, bivariate normal, no correlation

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1811] trunk/gplots/man/ci2d.Rd

From: <wa...@us...> - 2014-04-17 19:03:13

Revision: 1811
          http://sourceforge.net/p/r-gregmisc/code/1811
Author:   warnes
Date:     2014-04-17 19:03:08 +0000 (Thu, 17 Apr 2014)
Log Message:
-----------
Add reference to r2d2::conf2d.

Modified Paths:
--------------
    trunk/gplots/man/ci2d.Rd

Modified: trunk/gplots/man/ci2d.Rd
===================================================================
--- trunk/gplots/man/ci2d.Rd	2014-04-17 17:33:31 UTC (rev 1810)
+++ trunk/gplots/man/ci2d.Rd	2014-04-17 19:03:08 UTC (rev 1811)
@@ -65,6 +65,10 @@
   Confidence intervals generated by ci2d are \emph{approximate}, and
   are subject to biases and/or artifacts induced by the binning or
   kernel smoothing method, bin locations, bin sizes, and kernel bandwidth.
+
+  The \code{\link[r2d2]{conf2d}} function in the \pkg{r2d2} package may create a more
+  accurate confidence region, and reports the actual proportion of
+  points inside the region.
   }
 \value{
   A \code{ci2d} object consisting of a list containing (at least) the
@@ -82,8 +86,8 @@
 }
 \author{ Gregory R. Warnes \email{gr...@wa...}}
 \seealso{
-  \code{\link[KernSmooth]{bkde2D}}, \code{\link[KernSmooth]{dpik}},
-  \code{\link{hist2d}}
+  \code{\link[KernSmooth]{bkde2D}}, \code{\link[r2d2]{conf2d}},
+  \code{\link[KernSmooth]{dpik}}, \code{\link{hist2d}}
 }
 \examples{
    ####

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1810] trunk/gtools/man/ASCIIfy.Rd

From: <wa...@us...> - 2014-04-17 17:33:33

Revision: 1810
          http://sourceforge.net/p/r-gregmisc/code/1810
Author:   warnes
Date:     2014-04-17 17:33:31 +0000 (Thu, 17 Apr 2014)
Log Message:
-----------
Update ASCIIfy man page to match source code and add keywords

Modified Paths:
--------------
    trunk/gtools/man/ASCIIfy.Rd

Modified: trunk/gtools/man/ASCIIfy.Rd
===================================================================
--- trunk/gtools/man/ASCIIfy.Rd	2014-04-17 17:25:53 UTC (rev 1809)
+++ trunk/gtools/man/ASCIIfy.Rd	2014-04-17 17:33:31 UTC (rev 1810)
@@ -6,10 +6,10 @@
   single-byte (\samp{\x00}) or two-byte (\samp{\u0000}) codes.
 }
 \usage{
-ASCIIfy(x, bytes = 2, fallback = "?")
+ASCIIfy(string, bytes = 2, fallback = "?")
 }
 \arguments{
-  \item{x}{a character vector, possibly containing non-ASCII
+  \item{string}{a character vector, possibly containing non-ASCII
     characters.}
   \item{bytes}{either \code{1} or \code{2}, for single-byte
     (\samp{\x00}) or two-byte (\samp{\u0000}) codes.}
@@ -44,4 +44,5 @@
 print(athens)
 ASCIIfy(athens)
 }
-\keyword{}
+\keyword{utilites}
+\keyword{character}

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1809] trunk/gtools/inst/NEWS

From: <wa...@us...> - 2014-04-17 17:25:55

Revision: 1809
          http://sourceforge.net/p/r-gregmisc/code/1809
Author:   warnes
Date:     2014-04-17 17:25:53 +0000 (Thu, 17 Apr 2014)
Log Message:
-----------
Update NEWS for gtools 3.4.0

Modified Paths:
--------------
    trunk/gtools/inst/NEWS

Modified: trunk/gtools/inst/NEWS
===================================================================
--- trunk/gtools/inst/NEWS	2014-04-17 16:56:34 UTC (rev 1808)
+++ trunk/gtools/inst/NEWS	2014-04-17 17:25:53 UTC (rev 1809)
@@ -1,3 +1,13 @@
+gtools 3.4.0 - 2014-04-14
+-------------------------
+
+New features:
+
+- New ASCIIfy() function to converts character vectors to ASCII
+  representation by escaping them as \x00 or \u0000 codes.
+  Contributed by Arni Magnusson.
+
+
 gtools 3.3.1 - 2014-03-01
 -------------------------
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1808] trunk/gtools

From: <wa...@us...> - 2014-04-17 16:56:37

Revision: 1808
          http://sourceforge.net/p/r-gregmisc/code/1808
Author:   warnes
Date:     2014-04-17 16:56:34 +0000 (Thu, 17 Apr 2014)
Log Message:
-----------
Add ASCIIfy function posted to RDevel by Arni Magnusson

Modified Paths:
--------------
    trunk/gtools/DESCRIPTION
    trunk/gtools/NAMESPACE

Added Paths:
-----------
    trunk/gtools/R/ASCIIfy.R
    trunk/gtools/man/ASCIIfy.Rd

Modified: trunk/gtools/DESCRIPTION
===================================================================
--- trunk/gtools/DESCRIPTION	2014-04-10 02:32:21 UTC (rev 1807)
+++ trunk/gtools/DESCRIPTION	2014-04-17 16:56:34 UTC (rev 1808)
@@ -1,8 +1,8 @@
 Package: gtools
 Title: Various R programming tools
 Description: Various R programming tools
-Version: 3.3.1
-Date: 2014-03-01
+Version: 3.4.0
+Date: 2014-04-15
 Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
 Maintainer: Gregory R. Warnes <gr...@wa...>
 License: LGPL-2.1

Modified: trunk/gtools/NAMESPACE
===================================================================
--- trunk/gtools/NAMESPACE	2014-04-10 02:32:21 UTC (rev 1807)
+++ trunk/gtools/NAMESPACE	2014-04-17 16:56:34 UTC (rev 1808)
@@ -4,6 +4,7 @@
        addLast,
        ask,
        assert,
+       ASCIIfy,
        binsearch,
        capture,
        checkRVersion,

Added: trunk/gtools/R/ASCIIfy.R
===================================================================
--- trunk/gtools/R/ASCIIfy.R	                        (rev 0)
+++ trunk/gtools/R/ASCIIfy.R	2014-04-17 16:56:34 UTC (rev 1808)
@@ -0,0 +1,39 @@
+ASCIIfy <- function(string, bytes=2, fallback="?")
+{
+  bytes <- match.arg(as.character(bytes), 1:2)
+  convert <- function(char)  # convert to ASCII, e.g. "z", "\xfe", or "\u00fe"
+  {
+    raw <- charToRaw(char)
+    if(length(raw)==1 && raw<=127)  # 7-bit
+      ascii <- char
+    else if(length(raw)==1 && bytes==1)  # 8-bit to \x00
+      ascii <- paste0("\\x", raw)
+    else if(length(raw)==1 && bytes==2)  # 8-bit to \u0000
+      ascii <- paste0("\\u", chartr(" ","0",formatC(as.character(raw),width=4)))
+    else if(length(raw)==2 && bytes==1)  # 16-bit to \x00, if possible
+      if(utf8ToInt(char) <= 255)
+        ascii <- paste0("\\x", format.hexmode(utf8ToInt(char)))
+      else {
+        ascii <- fallback; warning(char, " could not be converted to 1 byte")}
+    else if(length(raw)==2 && bytes==2)  # UTF-8 to \u0000
+      ascii <- paste0("\\u", format.hexmode(utf8ToInt(char),width=4))
+    else {
+      ascii <- fallback
+      warning(char, " could not be converted to ", bytes, " byte")}
+    return(ascii)
+  }
+
+  if(length(string) > 1)
+  {
+    sapply(string, ASCIIfy, bytes=bytes, fallback=fallback, USE.NAMES=FALSE)
+  }
+  else
+  {
+    input <- unlist(strsplit(string,""))  # "c"  "a"  "f"  "<\'e>"
+    output <- character(length(input))    # ""   ""   ""   ""
+    for(i in seq_along(input))
+      output[i] <- convert(input[i])      # "c"  "a"  "f"  "\\u00e9"
+    output <- paste(output, collapse="")  # "caf\\u00e9"
+    return(output)
+  }
+}

Added: trunk/gtools/man/ASCIIfy.Rd
===================================================================
--- trunk/gtools/man/ASCIIfy.Rd	                        (rev 0)
+++ trunk/gtools/man/ASCIIfy.Rd	2014-04-17 16:56:34 UTC (rev 1808)
@@ -0,0 +1,47 @@
+\name{ASCIIfy}
+\alias{ASCIIfy}
+\title{Convert Characters to ASCII}
+\description{
+  Convert character vector to ASCII, replacing non-ASCII characters with
+  single-byte (\samp{\x00}) or two-byte (\samp{\u0000}) codes.
+}
+\usage{
+ASCIIfy(x, bytes = 2, fallback = "?")
+}
+\arguments{
+  \item{x}{a character vector, possibly containing non-ASCII
+    characters.}
+  \item{bytes}{either \code{1} or \code{2}, for single-byte
+    (\samp{\x00}) or two-byte (\samp{\u0000}) codes.}
+  \item{fallback}{an output character to use, when input characters
+    cannot be converted.}
+}
+\value{
+  A character vector like \code{x}, except non-ASCII characters have
+  been replaced with \samp{\x00} or \samp{\u0000} codes.
+}
+\author{Arni Magnusson \email{ar...@ha...}}
+\note{
+  To render single backslashes, use these or similar techniques:
+  \verb{
+    write(ASCIIfy(x), "file.txt")
+    cat(paste(ASCIIfy(x), collapse="\n"), "\n", sep="")}
+
+  The resulting strings are plain ASCII and can be used in R functions
+  and datasets to improve package portability.
+}
+\seealso{
+  \code{\link[tools]{showNonASCII}} identifies non-ASCII characters in
+  a character vector.
+}
+\examples{
+cities <- c("S\u00e3o Paulo", "Reykjav\u00edk")
+print(cities)
+ASCIIfy(cities, 1)
+ASCIIfy(cities, 2)
+
+athens <- "\u0391\u03b8\u03ae\u03bd\u03b1"
+print(athens)
+ASCIIfy(athens)
+}
+\keyword{}

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1807] trunk/SASxport/tests/dfAttributes.R

From: <wa...@us...> - 2014-04-10 02:32:23

Revision: 1807
          http://sourceforge.net/p/r-gregmisc/code/1807
Author:   warnes
Date:     2014-04-10 02:32:21 +0000 (Thu, 10 Apr 2014)
Log Message:
-----------
Oops.  Correct over-zealous paste.

Modified Paths:
--------------
    trunk/SASxport/tests/dfAttributes.R

Modified: trunk/SASxport/tests/dfAttributes.R
===================================================================
--- trunk/SASxport/tests/dfAttributes.R	2014-04-10 02:29:46 UTC (rev 1806)
+++ trunk/SASxport/tests/dfAttributes.R	2014-04-10 02:32:21 UTC (rev 1807)
@@ -30,8 +30,8 @@
 label(abc.out, self=TRUE, "MISSING!")
 label(abc.in , self=TRUE, "MISSING!")
 
-SAStype(abc.out, self=TRUE, "MISSING!")
-SAStype(abc.in , self=TRUE, "MISSING!")
+SAStype(abc.out, "MISSING!")
+SAStype(abc.in , "MISSING!")
 
 stopifnot( label  (abc.out, self=TRUE, "MISSING!") ==
            label  (abc.in,  self=TRUE, "MISSING!") )

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1806] trunk/SASxport/tests/dfAttributes.R

From: <wa...@us...> - 2014-04-10 02:29:48

Revision: 1806
          http://sourceforge.net/p/r-gregmisc/code/1806
Author:   warnes
Date:     2014-04-10 02:29:46 +0000 (Thu, 10 Apr 2014)
Log Message:
-----------
Update test to use new 'self' argument for label data.frame method.

Modified Paths:
--------------
    trunk/SASxport/tests/dfAttributes.R

Modified: trunk/SASxport/tests/dfAttributes.R
===================================================================
--- trunk/SASxport/tests/dfAttributes.R	2014-04-10 02:11:45 UTC (rev 1805)
+++ trunk/SASxport/tests/dfAttributes.R	2014-04-10 02:29:46 UTC (rev 1806)
@@ -5,7 +5,7 @@
 abc.out <- data.frame( x=c(1, 2, NA, NA ), y=c('a', 'B', NA, '*' ) )
 
 ## add a data set label (not used by R)
-label(abc.out) <- "xxxx data set xxxxx"
+label(abc.out, self=TRUE) <- "xxxx data set xxxxx"
 SAStype(abc.out) <- "normal"
 
 ## add a format specifier (not used by R)
@@ -27,13 +27,16 @@
 abc.in <- read.xport("dfAttributes.xpt", names.tolower=FALSE)
 
 ## Test that the files are otherwise identical
-label(abc.out, "MISSING!")
-label(abc.in , "MISSING!")
+label(abc.out, self=TRUE, "MISSING!")
+label(abc.in , self=TRUE, "MISSING!")
 
-SAStype(abc.out, "MISSING!")
-SAStype(abc.in , "MISSING!")
+SAStype(abc.out, self=TRUE, "MISSING!")
+SAStype(abc.in , self=TRUE, "MISSING!")
 
-stopifnot( label  (abc.out, "MISSING!")==label  (abc.in, "MISSING!") )
-stopifnot( SAStype(abc.out, "MISSING!")==SAStype(abc.in, "MISSING!") )
+stopifnot( label  (abc.out, self=TRUE, "MISSING!") ==
+           label  (abc.in,  self=TRUE, "MISSING!") )
 
+stopifnot( SAStype(abc.out, "MISSING!") ==
+           SAStype(abc.in,  "MISSING!") )
 
+

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1805] trunk/SASxport

From: <wa...@us...> - 2014-04-10 02:11:49

Revision: 1805
          http://sourceforge.net/p/r-gregmisc/code/1805
Author:   warnes
Date:     2014-04-10 02:11:45 +0000 (Thu, 10 Apr 2014)
Log Message:
-----------
Update for SASxport 1.4.0.

Modified Paths:
--------------
    trunk/SASxport/DESCRIPTION
    trunk/SASxport/inst/NEWS

Modified: trunk/SASxport/DESCRIPTION
===================================================================
--- trunk/SASxport/DESCRIPTION	2014-04-10 02:03:19 UTC (rev 1804)
+++ trunk/SASxport/DESCRIPTION	2014-04-10 02:11:45 UTC (rev 1805)
@@ -1,7 +1,7 @@
 Package: SASxport
 Type: Package
 Title: Read and Write SAS XPORT Files
-Version: 1.3.7
+Version: 1.4.0
 Date: 2014-04-09
 Description: This package provides functions for reading, listing
   the contents of, and writing SAS xport format files.

Modified: trunk/SASxport/inst/NEWS
===================================================================
--- trunk/SASxport/inst/NEWS	2014-04-10 02:03:19 UTC (rev 1804)
+++ trunk/SASxport/inst/NEWS	2014-04-10 02:11:45 UTC (rev 1805)
@@ -1,3 +1,20 @@
+Version 1.4.0 - 2014-04-09
+--------------------------
+
+API Change:
+
+- SASxport now relies on the 'label' methods defined by the Hmisc
+  package instead of defining its own.
+
+Bug fixes:
+
+- The 'read.xport' and 'write.xport' functions were failing when both
+  the SASxport and the Hmisc packages were loaded due to conflicts
+  between the label methods defined by each package.  This has been
+  resolved by removing the label methods from SASxport and using those
+  from Hmisc instead.
+
+
 Version 1.3.6 2013-10-09
 ------------------------
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1804] trunk/SASxport

From: <wa...@us...> - 2014-04-10 02:03:22

Revision: 1804
          http://sourceforge.net/p/r-gregmisc/code/1804
Author:   warnes
Date:     2014-04-10 02:03:19 +0000 (Thu, 10 Apr 2014)
Log Message:
-----------
Remove definitions of labels in favor of those coming from Hmisc.  Modify read.xport and write.xport to use appropriate arguments for label method for data.frames.

Modified Paths:
--------------
    trunk/SASxport/DESCRIPTION
    trunk/SASxport/NAMESPACE

Modified: trunk/SASxport/DESCRIPTION
===================================================================
--- trunk/SASxport/DESCRIPTION	2014-04-10 02:02:25 UTC (rev 1803)
+++ trunk/SASxport/DESCRIPTION	2014-04-10 02:03:19 UTC (rev 1804)
@@ -1,8 +1,8 @@
 Package: SASxport
 Type: Package
 Title: Read and Write SAS XPORT Files
-Version: 1.3.6
-Date: 2013-10-09
+Version: 1.3.7
+Date: 2014-04-09
 Description: This package provides functions for reading, listing
   the contents of, and writing SAS xport format files.
   The functions support reading and writing of either
@@ -38,5 +38,5 @@
   <http://metruminstitute.org>.
 Maintainer: Gregory R. Warnes <gr...@wa...>
 License: GPL-2
-Depends: R (>= 2.4.0), chron
+Depends: R (>= 2.4.0), chron, Hmisc
 URL: http://www.warnes.net, http://metruminstitute.org

Modified: trunk/SASxport/NAMESPACE
===================================================================
--- trunk/SASxport/NAMESPACE	2014-04-10 02:02:25 UTC (rev 1803)
+++ trunk/SASxport/NAMESPACE	2014-04-10 02:03:19 UTC (rev 1804)
@@ -2,20 +2,21 @@
 
 importFrom(chron, chron, times)
 importFrom(utils, packageDescription)
+importFrom(Hmisc, label, "label<-")
 
 export(
        toSAS,
        lookup.xport,
        read.xport,
        write.xport,
-       "label",
-       "label<-",
+       ## "label",
+       ## "label<-",
 
        makeSASNames,
-       
+
        "SASformat",
        "SASformat<-",
-       
+
        "SASiformat",
        "SASiformat<-",
 
@@ -32,12 +33,12 @@
 S3method(toSAS, Date)
 S3method(toSAS, default)
 
-S3method(label, default)
+## S3method(label, default)
 S3method(SASformat, default)
 S3method(SASiformat, default)
 S3method(SAStype, default)
 
-S3method("label<-", default)
+## S3method("label<-", default)
 S3method("SASformat<-", default)
 S3method("SASiformat<-", default)
 S3method("SAStype<-", default)

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1803] trunk/SASxport

From: <wa...@us...> - 2014-04-10 02:02:29

Revision: 1803
          http://sourceforge.net/p/r-gregmisc/code/1803
Author:   warnes
Date:     2014-04-10 02:02:25 +0000 (Thu, 10 Apr 2014)
Log Message:
-----------
Remove definitions of labels in favor of those coming from Hmisc.  Modify read.xport and write.xport to use appropriate arguments for label method for data.frames.

Modified Paths:
--------------
    trunk/SASxport/R/read.xport.R
    trunk/SASxport/R/write.xport.R

Removed Paths:
-------------
    trunk/SASxport/R/label.R
    trunk/SASxport/man/label.Rd

Deleted: trunk/SASxport/R/label.R
===================================================================
--- trunk/SASxport/R/label.R	2014-04-09 23:52:17 UTC (rev 1802)
+++ trunk/SASxport/R/label.R	2014-04-10 02:02:25 UTC (rev 1803)
@@ -1,20 +0,0 @@
-label <- function(x, default)
-  UseMethod("label")
-
-label.default <- function(x, default=NULL)
-{
-  lab <- attr(x,"label")
-  if(is.null(lab))
-    default
-  else
-  lab
-}
-
-"label<-" <- function(x, value)
-  UseMethod("label<-")
-
-"label<-.default" <- function(x, value)
-{
-  attr(x,'label') <- value
-  x
-}

Modified: trunk/SASxport/R/read.xport.R
===================================================================
--- trunk/SASxport/R/read.xport.R	2014-04-09 23:52:17 UTC (rev 1802)
+++ trunk/SASxport/R/read.xport.R	2014-04-10 02:02:25 UTC (rev 1803)
@@ -1,5 +1,5 @@
 ##
-## Code originally from Frank Harrell's 'Hmisc' library: 
+## Code originally from Frank Harrell's 'Hmisc' library:
 ##   http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/Hmisc
 ## Copied with permission on 2007-08-04
 ##
@@ -32,7 +32,7 @@
 
     if(length(grep('http://', file))>0 || length(grep('ftp://', file))>0 )
       {
-        scat("Downloading file...")        
+        scat("Downloading file...")
         tf <- tempfile()
         download.file(file, tf, mode='wb', quiet=TRUE)
         file <- tf
@@ -44,13 +44,13 @@
     file.header <- substr(file.header, start=1, stop=nchar(xport.file.header) )
     if( !identical(xport.file.header, file.header) )
       stop("The specified file does not start with a SAS xport file header!")
-           
+
     scat("Extracting data file information...")
     dsinfo <- lookup.xport.inner(file)
 
     dsLabels <- sapply(dsinfo, label)
     dsTypes  <- sapply(dsinfo, SAStype)
-    
+
     if(length(keep))
       whichds <- toupper(keep)
     else
@@ -65,7 +65,7 @@
          names(ds) <- make.unique(names(ds))
        }
 
-    
+
     if( (length(keep)>0 || length(drop)>0) )
       ds <- ds[whichds]
 
@@ -82,7 +82,7 @@
         fds <- fds[1]
       }
     }
-  
+
     finfo <- NULL
     if(length(formats) || length(fds)) {
       if(length(formats))
@@ -108,7 +108,7 @@
     names(res) <- gsub('_','.',dsn)
 
 
-    possiblyConvertChar <- (is.logical(as.is) && !as.is) || 
+    possiblyConvertChar <- (is.logical(as.is) && !as.is) ||
                            (is.numeric(as.is) && as.is > 0)
     j <- 0
     for(k in which.regular) {
@@ -120,9 +120,9 @@
         else ds[[k]]
 
       scat('.')
-      
-      label(w)   <- dsLabels[k]
-      names(label(w)) <- NULL
+
+      label(w, self=TRUE)   <- dsLabels[k]
+      names(label(w, self=TRUE)) <- NULL
       SAStype(w) <- dsTypes[k]
       names(SAStype(w)) <- NULL
 
@@ -137,7 +137,7 @@
       iformats <- fstr( ifmt, dinfo$iflength, dinfo$ifdigits)
 
       lab      <- dinfo$label
-      
+
       ndinfo   <- names.tolower(makeNames(dinfo$name, allow=name.chars))
       names(lab) <- names(fmt) <- names(formats) <- names(iformats) <- ndinfo
       if(length(w)>0)
@@ -176,13 +176,13 @@
             }
             }
           } else if(possiblyConvertChar && is.character(x)) {
-            if((is.logical(as.is) && !as.is) || 
+            if((is.logical(as.is) && !as.is) ||
                (is.numeric(as.is) && length(unique(x)) < as.is*length(x))) {
               x <- factor(x, exclude='')
               changed <- TRUE
             }
           }
-          
+
           lz <- lab[nam[i]]
           if(!is.null(lz) && length(lz)>0 && !is.na(lz) && lz != '') {
             names(lz) <- NULL
@@ -195,13 +195,13 @@
               SASformat(x) <- formats[[nam[i]]]
               changed <- TRUE
             }
-          
+
           if(nam[i] %in% names(iformats) && iformats[nam[i]] > "" )
             {
               SASformat(x) <- formats[[nam[i]]]
             changed <- TRUE
             }
-          
+
           if(changed)
             w[[i]] <- x
         }
@@ -216,7 +216,7 @@
     if( include.formats )
       {
         nds <- nds+1
-        if( length(fds)>0 ) 
+        if( length(fds)>0 )
           res$"FORMATS" <- ds[[fds]]
         else
           res$FORMATS <- empty.format.table()

Modified: trunk/SASxport/R/write.xport.R
===================================================================
--- trunk/SASxport/R/write.xport.R	2014-04-09 23:52:17 UTC (rev 1802)
+++ trunk/SASxport/R/write.xport.R	2014-04-10 02:02:25 UTC (rev 1803)
@@ -1,13 +1,13 @@
 write.xport <- function(...,
                         list=base::list(),
-                        file = stop("'file' must be specified"), 
+                        file = stop("'file' must be specified"),
                         verbose=FALSE,
                         sasVer="7.00",
                         osType,
                         cDate=Sys.time(),
                         formats=NULL,
                         autogen.formats=TRUE
-                        ) 
+                        )
   {
 
     ## Handle verbose option ##
@@ -31,10 +31,10 @@
     dotNames <- names(dotList)
     if(is.null(dotNames)) dotNames <- rep("", length(dotList))
 
-    if(length(dotList)>0) 
+    if(length(dotList)>0)
       {
         ## Get data frame names from ... in function call, but don't
-        ## clobber any explicitly provided names 
+        ## clobber any explicitly provided names
         mc <- match.call()
         mc$file <- NULL
         mc$verbose <- NULL
@@ -45,8 +45,8 @@
         mc$autogen.formats <- NULL
         mc[[1]] <- NULL
         # note we *do not* mask off format argument so it will get
-        # magically included if present.  
-    
+        # magically included if present.
+
         mc <- as.character(mc)
 
         badNames <- which(is.na(dotNames) | dotNames<="")
@@ -59,7 +59,7 @@
       listNames <- rep("", length(list))
     dfList  <- c(dotList, list)
     dfNames <- c(dotNames, listNames)
-    
+
     ## check for and handle <NA> or empty names ##
     badNames <- which(is.na(dfNames) | dfNames<="")
     if(length(badNames)>0)
@@ -79,7 +79,7 @@
       if(length(not.df)==1)
         stop(paste("'", dfNames[not.df], "'"),
              " is not a data.frame object.")
-      else 
+      else
         stop(paste("'", dfNames[not.df], "'", sep="", collapse=", "),
              " are not data.frame objects.")
     ##
@@ -111,8 +111,8 @@
 
     #######
     scat("opening file ...")
-    if (is.character(file)) 
-      if (file == "") 
+    if (is.character(file))
+      if (file == "")
         file <- stdout()
       else {
         file <- file(description=file, open="wb")
@@ -132,10 +132,10 @@
     scat("Write file header ...")
     out( xport.file.header( cDate=cDate, sasVer=sasVer, osType=osType ) )
     scat("Done.")
-    
+
     for(i in dfNames)
       {
-        
+
         df <- dfList[[i]]
 
         if(is.null(colnames(df)))
@@ -149,17 +149,17 @@
             dfList[[i]] <- df
           }
 
-        
+
         colnames(dfList[[i]]) <- colnames(df) <- varNames <- makeSASNames(colnames(df))
-        
+
         offsetTable <- data.frame("name"=varNames,
                                   "len"=rep(NA, length(varNames)),
                                   "offset"=rep(NA, length(varNames)) )
         rownames(offsetTable) <- offsetTable[,"name"]
 
-        dfLabel <- label(df, default="" )
+        dfLabel <- label(df, default="", self=TRUE )
         dfType <- SAStype(df, default="")
-        
+
         scat("Write data frame header ...")
         out( xport.member.header(dfName=i, cDate=cDate, sasVer=sasVer, osType=osType,
                                  dfLabel=dfLabel, dfType=dfType) )
@@ -168,7 +168,7 @@
         scat("Write variable information block header ...")
         out( xport.namestr.header( nvar=ncol(df) ) )
         scat("Done.")
-        
+
         scat("Write entries for variable information block ...")
         lenIndex <- 0
         varIndex <- 1
@@ -197,14 +197,14 @@
             offsetTable[i, "offset"] <- lenIndex
 
 
-            
 
+
             # parse format and iformat
             formatInfo  <- parseFormat(varFormat)
             iFormatInfo <- parseFormat(varIFormat)
-            
-            
-            
+
+
+
             # write the entry
             out(
                 xport.namestr(
@@ -213,7 +213,7 @@
                               varNum    = varIndex,
                               varPos    = lenIndex,
                               varLength = varLen,
-                              varLabel  = varLabel,        
+                              varLabel  = varLabel,
                               fName   = formatInfo$name,
                               fLength = formatInfo$len,
                               fDigits = formatInfo$digits,
@@ -232,8 +232,8 @@
 
         # Space-fill to 80 character record end
         fillSize <- 80 - (spaceUsed %% 80)
-        if(fillSize==80) fillSize <- 0        
-        out( xport.fill( TRUE, fillSize ) ) 
+        if(fillSize==80) fillSize <- 0
+        out( xport.fill( TRUE, fillSize ) )
 
         scat("Write header for data block ...")
         out( xport.obs.header() )
@@ -248,7 +248,7 @@
               {
                 val <- df[i,j]
                 valLen <- offsetTable[j,"len"]
-                
+
                 scat("i=", i, " j=", j, " value=", val, " len=", valLen, "");
                 if(is.character( val ))
                   {
@@ -260,18 +260,18 @@
                 spaceUsed <- spaceUsed + valLen
               }
         }
-        
+
         fillSize <- 80 - (spaceUsed %% 80)
         if(fillSize==80) fillSize <- 0
         out( xport.fill(TRUE, fillSize ) )
-        
+
         scat("Done.")
       }
 
     scat("Closing file ...")
-    if (is.character(file)) 
+    if (is.character(file))
       if (file != "")
-        {        
+        {
           close(file)
           on.exit()
         }

Deleted: trunk/SASxport/man/label.Rd
===================================================================
--- trunk/SASxport/man/label.Rd	2014-04-09 23:52:17 UTC (rev 1802)
+++ trunk/SASxport/man/label.Rd	2014-04-10 02:02:25 UTC (rev 1803)
@@ -1,107 +0,0 @@
-\name{label}
-
-\alias{label}
-\alias{label.default}
-\alias{label<-}
-\alias{label<-.default}
-
-\alias{SASformat}
-\alias{SASformat.default}
-\alias{SASformat<-}
-\alias{SASformat<-.default}
-
-\alias{SASiformat}
-\alias{SASiformat.default}
-\alias{SASiformat<-}
-\alias{SASiformat<-.default}
-
-\alias{SAStype}
-\alias{SAStype.default}
-\alias{SAStype<-}
-\alias{SAStype<-.default}
-
-\title{
-Set or Retreive the 'label', 'SASformat', 'SASiformat', or 'SAStype'
-attribute of a vector or (components of) a data frame
-}
-\description{
-  Sets or retrieves the \code{"label"}, \code{"SASformat"}, 
-  \code{"SASiformat"}, or \code{SAStype} attribute of an object.
-
-  More comprehensive support for object labels, and SASformat, are
-  available in Frank Harrell's \code{Hmisc} package.
-
-  Note that \code{SAStype} enforces the SAS 8-character naming convention.
-}
-\usage{
-label(x, default)
-label(x) <- value
-
-SASformat(x, default)
-SASformat(x) <- value
-
-SASiformat(x, default)
-SASiformat(x) <- value
-
-SAStype(x, default)
-SAStype(x) <- value
-}
-\arguments{
-\item{x}{any object}
-\item{value}{new value for the  \code{"label"}, \code{"SASformat"}, 
-  \code{"SASiformat"}, or \code{SAStype}  attribute of an object.}
-\item{default}{value to return when no appropriate attribute is
-  found.  The usual return value is NULL.}
-}
-\value{
-  the contents of the \code{"label"}, \code{"SASformat"},
-  \code{"SASiformat"}, \code{"SAStype"} attribute of x, if any;
-  otherwise, the value provided by \code{default}.
-}
-\author{
-  Gregory R. Warnes \email{gr...@wa...} based on code from the
-  \code{Hmisc} library by Frank E. Harrell, Jr.  ]
-}
-%\seealso{
-%}
-\examples{
-
-## Examples for vectors
-
-fail.time <- c(10,20)
-
-# set attributes
-label(fail.time) <- 'Failure Time'
-SASformat(fail.time) <- 'Numeric2'
-SASiformat(fail.time) <- 'Numeric2'
-
-# display individual attributes
-label(fail.time)
-SASformat(fail.time)
-SASiformat(fail.time)
-
-# display all attributes
-attributes(fail.time)
-
-## SAStype only applies to data frames
-df <- data.frame( fail.time, day=c("Mon","Tue") )
-label(df)   <- "Data frame object"
-SAStype(df) <- "USER"
-
-label(df)
-SAStype(df)
-
-## Example showing specification of default return value
-a <- 70
-label(a, default="no label")
-
-\dontrun{
-# Hmisc packages functions label attributes for annotating tables and plots:
-library(Hmisc)
-label(fail.time)
-describe(fail.time)
-}
-}
-\keyword{utilities}
-\keyword{interface}
-

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1802] trunk/gplots/R/heatmap.2.R

From: <wa...@us...> - 2014-04-09 23:52:19

Revision: 1802
          http://sourceforge.net/p/r-gregmisc/code/1802
Author:   warnes
Date:     2014-04-09 23:52:17 +0000 (Wed, 09 Apr 2014)
Log Message:
-----------
Add padj=0.5 to better align margin labels.

Modified Paths:
--------------
    trunk/gplots/R/heatmap.2.R

Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R	2014-04-05 21:08:41 UTC (rev 1801)
+++ trunk/gplots/R/heatmap.2.R	2014-04-09 23:52:17 UTC (rev 1802)
@@ -66,6 +66,12 @@
                        denscol=tracecol,
                        symkey = min(x < 0, na.rm=TRUE) || symbreaks,
                        densadj = 0.25,
+                       key.title = NULL,
+                       key.xlab = NULL,
+                       key.ylab = NULL,
+                       key.xtickfun = NULL,
+                       key.ytickfun = NULL,
+                       key.par=list(),
 
                        ## plot labels
                        main = NULL,
@@ -562,7 +568,16 @@
   ## Add the color-key
   if(key)
     {
-      par(mar = c(5, 4, 2, 1), cex=0.75)
+      mar <- c(5, 4, 2, 1)
+      if (!is.null(key.xlab) && is.na(key.xlab))
+          mar[1] <- 2
+      if (!is.null(key.ylab) && is.na(key.ylab))
+          mar[2] <- 2
+      if (!is.null(key.title) && is.na(key.title))
+          mar[3] <- 1
+      par(mar = mar, cex=0.75, mgp=c(2, 1, 0))
+      if (length(key.par) > 0)
+          do.call(par, key.par)
       tmpbreaks <- breaks
 
       if(symkey)
@@ -584,15 +599,26 @@
             xaxt="n", yaxt="n")
 
       par(usr=c(0,1,0,1))
-      lv <- pretty(breaks)
-      xv <- scale01(as.numeric(lv), min.raw, max.raw)
-      axis(1, at=xv, labels=lv)
-      if(scale=="row")
-        mtext(side=1,"Row Z-Score", line=2)
-      else if(scale=="column")
-        mtext(side=1,"Column Z-Score", line=2)
-      else
-        mtext(side=1,"Value", line=2)
+      if (is.null(key.xtickfun)) {
+          lv <- pretty(breaks)
+          xv <- scale01(as.numeric(lv), min.raw, max.raw)
+          xargs <- list(at=xv, labels=lv)
+      } else {
+          xargs <- key.xtickfun()
+      }
+      xargs$side <- 1
+      do.call(axis, xargs)
+      if (is.null(key.xlab)) {
+        if(scale=="row")
+            key.xlab <- "Row Z-Score"
+        else if(scale=="column")
+           key.xlab <- "Column Z-Score"
+        else
+            key.xlab <- "Value"
+      }
+      if (!is.na(key.xlab)) {
+          mtext(side=1, key.xlab, line=par("mgp")[1], padj=0.5)
+      }
 
       if(density.info=="density")
         {
@@ -602,10 +628,22 @@
           dens$y <- dens$y[-omit]
           dens$x <- scale01(dens$x, min.raw, max.raw)
           lines(dens$x, dens$y / max(dens$y) * 0.95, col=denscol, lwd=1)
-          axis(2, at=pretty(dens$y)/max(dens$y) * 0.95, pretty(dens$y) )
-          title("Color Key\nand Density Plot")
+          if (is.null(key.ytickfun)) {
+              yargs <- list(at=pretty(dens$y)/max(dens$y) * 0.95, labels=pretty(dens$y))
+          } else {
+              yargs <- key.ytickfun()
+          }
+          yargs$side <- 2
+          do.call(axis, yargs)
+          if (is.null(key.title))
+              key.title <- "Color Key\nand Density Plot"
+          if (!is.na(key.title))
+            title(key.title)
           par(cex=0.5)
-          mtext(side=2,"Density", line=2)
+          if (is.null(key.ylab))
+              key.ylab <- "Density"
+          if (!is.na(key.ylab))
+            mtext(side=2,key.ylab, line=par("mgp")[1], padj=0.5)
         }
       else if(density.info=="histogram")
         {
@@ -613,10 +651,22 @@
           hx <- scale01(breaks, min.raw, max.raw)
           hy <- c(h$counts, h$counts[length(h$counts)])
           lines(hx, hy/max(hy)*0.95, lwd=1, type="s", col=denscol)
-          axis(2, at=pretty(hy)/max(hy) * 0.95, pretty(hy) )
-          title("Color Key\nand Histogram")
+          if (is.null(key.ytickfun)) {
+              yargs <- list(at=pretty(hy)/max(hy) * 0.95, labels=pretty(hy))
+          } else {
+              yargs <- key.ytickfun()
+          }
+          yargs$side <- 2
+          do.call(axis, yargs)
+          if (is.null(key.title))
+              key.title <- "Color Key\nand Histogram"
+          if (!is.na(key.title))
+            title(key.title)
           par(cex=0.5)
-          mtext(side=2,"Count", line=2)
+          if (is.null(key.ylab))
+              key.ylab <- "Count"
+          if (!is.na(key.ylab))
+            mtext(side=2,key.ylab, line=par("mgp")[1], padj=0.5)
         }
       else
         title("Color Key")

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