r-gregmisc-users — Discussion list for R gregmisc packages (gplot, gmodels, gdata, gtools)

[R-gregmisc-users] SF.net SVN: r-gregmisc:[1954] trunk/gplots

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

Revision: 1954
          http://sourceforge.net/p/r-gregmisc/code/1954
Author:   warnes
Date:     2015-04-23 22:55:43 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
In heatmap.2(), the color key now properly handles color breaks that
are not equally spaced.  (Issue reported by Tim Richter-Heitmann.)

Modified Paths:
--------------
    trunk/gplots/DESCRIPTION
    trunk/gplots/R/heatmap.2.R
    trunk/gplots/inst/ChangeLog
    trunk/gplots/inst/NEWS

Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION	2015-04-23 22:49:10 UTC (rev 1953)
+++ trunk/gplots/DESCRIPTION	2015-04-23 22:55:43 UTC (rev 1954)
@@ -5,7 +5,7 @@
 Imports: gtools, gdata, stats, caTools, KernSmooth
 Suggests: grid, MASS
 Version: 2.17.0
-Date: 2015-04-21
+Date: 2015-04-23
 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/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R	2015-04-23 22:49:10 UTC (rev 1953)
+++ trunk/gplots/R/heatmap.2.R	2015-04-23 22:55:43 UTC (rev 1954)
@@ -198,8 +198,8 @@
           nr <- length(rowInd)
     }
   else if (is.integer(Rowv))
-    { ## Compute dendrogram and do reordering based on given vector
-        browser()
+    {
+      ## Compute dendrogram and do reordering based on given vector
       distr <- distfun(x)       
       hcr <- hclustfun(distr)
       ddr <- as.dendrogram(hcr)
@@ -641,7 +641,7 @@
           max.raw <- max.breaks
         }
 
-      z <- seq(min.raw, max.raw, length=length(col))
+      z <- seq(min.raw, max.raw, by=min(diff(breaks)/4))
       image(z=matrix(z, ncol=1),
             col=col, breaks=tmpbreaks,
             xaxt="n", yaxt="n")
@@ -670,10 +670,11 @@
 
       if(density.info=="density")
         {
-          dens <- density(x, adjust=densadj, na.rm=TRUE)
+          dens <- density(x, adjust=densadj, na.rm=TRUE,
+                          from=min.scale, to=max.scale)
           omit <- dens$x < min(breaks) | dens$x > max(breaks)
-          dens$x <- dens$x[-omit]
-          dens$y <- dens$y[-omit]
+          dens$x <- dens$x[!omit]
+          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)
           if (is.null(key.ytickfun)) {

Modified: trunk/gplots/inst/ChangeLog
===================================================================
--- trunk/gplots/inst/ChangeLog	2015-04-23 22:49:10 UTC (rev 1953)
+++ trunk/gplots/inst/ChangeLog	2015-04-23 22:55:43 UTC (rev 1954)
@@ -1,5 +1,36 @@
+2015-04-23  warnes
+
+	* [r1948] R/plotCI.R: - plotCI() was not properly respecting the
+	  'type=' argument. This has
+	  been corrected.
+	* [r1947] R/overplot.R: - Remove stray browser() call from
+	  overplot()
+	* [r1943] man/balloonplot.Rd: Explicitly specify argument to
+	  gplots:::reorder.factor to prevent error.
+	* [r1942] R/venn.R, man/venn.Rd: - 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'.
+	* [r1941] R/heatmap.2.R: Patch submitted by Ilia Kats:
+	  - easily extract and plot subclusters from a big heatmap using
+	  the
+	  same colorkey, by passing a dendgrogram of the subcluster
+	  together
+	  with the full data matrix and, optionally, the breaks of the full
+	  heatmap in order to obtain the same color scaling. This is useful
+	  if
+	  one wants to plot several subclusters as different panels in a
+	  paper, but maintain consistent color coding.
+	  - Improves the behavior of the color key axis labels, as they now
+	  honor par("cex") and par("cex.lab").
+	* [r1940] R/heatmap.2.R: In heatmap.2() split calls to distfun()
+	  and hclustfun() into separate steps to make debugging easier
+
 2015-04-22  warnes
 
+	* [r1931] DESCRIPTION, inst/ChangeLog, inst/NEWS: Update
+	  DESCRIPTION, ChangeLog, and NEWS for gplots 2.17.0
 	* [r1930] R/heatmap.2.R, man/heatmap.2.Rd: heatmap.2: add new
 	  'colRow' and 'colCol' arguments to control the color of row and
 	  column text labels

Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS	2015-04-23 22:49:10 UTC (rev 1953)
+++ trunk/gplots/inst/NEWS	2015-04-23 22:55:43 UTC (rev 1954)
@@ -1,4 +1,4 @@
-Release 2.17.0 - 2015-04-21
+Release 2.17.0 - 2015-04-23
 ---------------------------
 
 New Features:
@@ -6,7 +6,30 @@
 - heatmap.2() has two new arguments, 'colRow' and 'colCol' to control
   the color of row and column text labels.
 
+- heatmap.2() has been modified to make it easier to extract and plot
+  subclusters from a large heatmap. Simply pass the dendrogram of the
+  subcluster together with the full data matrix and, optionally, the
+  breaks of the full heatmap in order to obtain the same color
+  scaling. (Patch contributed by Ilia Kats.) 
 
+- venn() now returns a list of the members of each set intersection in
+  the attribute 'intersections'.  This can be disabled using the
+  argument 'intersection=FALSE' (Patch by Steffen Möller.)
+
+Bug Fixes:
+
+- plotCI() now properly respects the 'type=' argument.  (Bug report
+  and correction by Wiktor Żelazny.)
+
+- Remove stray browser() call from overplot()
+
+- In the balloonplot() examples, explicitly specify argument to
+  gplots:::reorder.factor to prevent error.
+
+Other Changes:
+
+- Remove stray browser() call from
+
 Release 2.16.0 - 2015-01-02
 ---------------------------
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1953] trunk/gdata/inst

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

Revision: 1953
          http://sourceforge.net/p/r-gregmisc/code/1953
Author:   warnes
Date:     2015-04-23 22:49:10 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
Update NEWS and ChangeLog

Modified Paths:
--------------
    trunk/gdata/inst/ChangeLog
    trunk/gdata/inst/NEWS

Modified: trunk/gdata/inst/ChangeLog
===================================================================
--- trunk/gdata/inst/ChangeLog	2015-04-23 22:41:46 UTC (rev 1952)
+++ trunk/gdata/inst/ChangeLog	2015-04-23 22:49:10 UTC (rev 1953)
@@ -1,5 +1,11 @@
 2015-04-23  warnes
 
+	* [r1952] R/write.fwf.R: - write.fwf() now properly supports
+	  matrix objects, including matrix objects wihtout column
+	  names. (Reported by Carl Witthoft.)
+	* [r1951] inst/perl/xls2csv.pl: Remove 'use POSIX' from xls2csv.pl
+	  since it is no longer needed
+	* [r1939] inst/ChangeLog, inst/NEWS: Update NEWS and ChangeLog
 	* [r1938] R/reorder.R: reorder.factor() now hands off processing to
 	  stats:::reorder.default() when either 'X' or 'FUN' is specified.
 

Modified: trunk/gdata/inst/NEWS
===================================================================
--- trunk/gdata/inst/NEWS	2015-04-23 22:41:46 UTC (rev 1952)
+++ trunk/gdata/inst/NEWS	2015-04-23 22:49:10 UTC (rev 1953)
@@ -29,15 +29,21 @@
   and providing either 'X' or 'FUN' causes processing to be handed off to 
   stats:::reorder.defailt() so will return the same results whether gdata
   is loaded or not.  (Reported by Sam Hunter.)
+
+- write.fwf() now properly supports matrix objects, including matrix
+  objects without column names. (Reported by Carl Witthoft.)
  
 Other changes:
 
-- Replaced depricated PERL function POSIX::isdigit with equivalent regular 
-  expression.
+- Replaced depricated PERL function POSIX::isdigit in xls2csv.pl
+  (which is used by read.xls() ) with an equivalent regular
+  expression. (Reported by both Charles Plessy, Gerrit-jan Schutten,
+  and Paul Johnson.  Charles also provided a patch to correct the
+  issue.)
 
 - object.size() now returns objects with S3 class 'object_sizes' (note the 
   final 's') to avoid conflicts with methods in utils for class 'object_size' 
-  which can only handle a scalar size.
+  provided by package 'utils' which can only handle a scalar size.
 
 
 Changes in 2.14.0 (2014-08-27)

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1952] trunk/gdata/R/write.fwf.R

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

Revision: 1952
          http://sourceforge.net/p/r-gregmisc/code/1952
Author:   warnes
Date:     2015-04-23 22:41:46 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
- write.fwf() now properly supports matrix objects, including matrix
  objects wihtout column names. (Reported by Carl Witthoft.)

Modified Paths:
--------------
    trunk/gdata/R/write.fwf.R

Modified: trunk/gdata/R/write.fwf.R
===================================================================
--- trunk/gdata/R/write.fwf.R	2015-04-23 21:55:42 UTC (rev 1951)
+++ trunk/gdata/R/write.fwf.R	2015-04-23 22:41:46 UTC (rev 1952)
@@ -44,6 +44,8 @@
     colnames(x)[1] <- rowColVal
   }
   colnamesMy <- colnames(x)
+  if(length(colnamesMy)==0)
+      colnamesMy <- paste( "V", 1:ncol(x), sep="")
 
   nRow <- nrow(x)
   nCol <- length(colnamesMy)
@@ -67,18 +69,20 @@
                           stringsAsFactors=FALSE)
 
   ## Which columns are numeric like
-  isNum <- sapply(x, is.numeric)
+  isNum <- apply(x, 2, is.numeric)
   ## is.numeric picks also Date and POSIXt
-  isNum <- isNum & !(sapply(x, inherits, what="Date") |
-                     sapply(x, inherits, what="POSIXt"))
+  isNum <- isNum & !(apply(x, 2, inherits, what="Date") |
+                     apply(x, 2, inherits, what="POSIXt"))
 
   ## Which columns are factors --> convert them to character
-  isFac <- sapply(x, is.factor)
-  x[, isFac] <- lapply(x[, isFac, drop=FALSE], as.character)
+  isFac <- apply(x, 2, is.factor)
+  x[, isFac] <- apply(x[, isFac, drop=FALSE], 2, as.character)
 
   ## Collect information about how format() will format columns.
   ## We need to get this info now, since format will turn all columns to character
-  tmp <- lapply(x, format.info, ...)
+browser()
+  
+  tmp <- apply(x, 2, format.info, ...)
   tmp1 <- sapply(tmp, length)
   tmp <- t(as.data.frame(tmp))
   retFormat$width <- tmp[, 1]
@@ -137,7 +141,7 @@
 
   ## Number of levels for "non-numeric"" columns
   if(any(!isNum)) {
-    retFormat[!isNum, "nlevels"] <- sapply(x[, !isNum, drop=FALSE],
+    retFormat[!isNum, "nlevels"] <- apply(x[, !isNum, drop=FALSE], 2,
                                            function(z) length(unique(z)))
   }
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1951] trunk/gdata/inst/perl/xls2csv.pl

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

Revision: 1951
          http://sourceforge.net/p/r-gregmisc/code/1951
Author:   warnes
Date:     2015-04-23 21:55:42 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
Remove 'use POSIX' from xls2csv.pl since it is no longer needed

Modified Paths:
--------------
    trunk/gdata/inst/perl/xls2csv.pl

Modified: trunk/gdata/inst/perl/xls2csv.pl
===================================================================
--- trunk/gdata/inst/perl/xls2csv.pl	2015-04-23 21:53:19 UTC (rev 1950)
+++ trunk/gdata/inst/perl/xls2csv.pl	2015-04-23 21:55:42 UTC (rev 1951)
@@ -9,7 +9,6 @@
 use strict;
 #use Spreadsheet::ParseExcel;
 #use Spreadsheet::ParseXLSX;
-use POSIX;
 use File::Spec::Functions;
 use Getopt::Std;
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1950] trunk/gtools/inst

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

Revision: 1950
          http://sourceforge.net/p/r-gregmisc/code/1950
Author:   warnes
Date:     2015-04-23 21:53:19 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
Update NEWS and ChangeLog

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

Modified: trunk/gtools/inst/ChangeLog
===================================================================
--- trunk/gtools/inst/ChangeLog	2015-04-23 21:47:48 UTC (rev 1949)
+++ trunk/gtools/inst/ChangeLog	2015-04-23 21:53:19 UTC (rev 1950)
@@ -1,5 +1,12 @@
 2015-04-23  warnes
 
+	* [r1949] R/quantcut.R, man/quantcut.Rd: - The 'q' argument to
+	  quantcut()'s 'q' now accept an integer
+	  indicating the number of equally spaced quantile groups to
+	  create. (Suggestion and patch submitted by Ryan C. Thompson.)
+	* [r1946] DESCRIPTION: Revers accidental text deletion:
+	* [r1945] DESCRIPTION, inst/ChangeLog, inst/NEWS: Update for gtools
+	  3.4.3
 	* [r1944] R/smartbind.R, R/strmacro.R: Remove debugging code and
 	  stray browser() call
 

Modified: trunk/gtools/inst/NEWS
===================================================================
--- trunk/gtools/inst/NEWS	2015-04-23 21:47:48 UTC (rev 1949)
+++ trunk/gtools/inst/NEWS	2015-04-23 21:53:19 UTC (rev 1950)
@@ -1,6 +1,12 @@
 gtools 3.4.3 - 2015-04-06
 -------------------------
 
+Enhancements:
+
+- The 'q' argument to quantcut() now accept an integer
+  indicating the number of equally spaced quantile groups to
+  create. (Suggestion and patch submitted by Ryan C. Thompson.)
+
 Bug fixes:
 
 - Removed stray browser() call in smartbind().

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1949] trunk/gtools

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

Revision: 1949
          http://sourceforge.net/p/r-gregmisc/code/1949
Author:   warnes
Date:     2015-04-23 21:47:48 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
- The 'q' argument to quantcut()'s 'q' now accept an integer
  indicating the number of equally spaced quantile groups to
  create. (Suggestion and patch submitted by Ryan C. Thompson.)

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

Modified: trunk/gtools/R/quantcut.R
===================================================================
--- trunk/gtools/R/quantcut.R	2015-04-23 21:23:36 UTC (rev 1948)
+++ trunk/gtools/R/quantcut.R	2015-04-23 21:47:48 UTC (rev 1949)
@@ -1,7 +1,10 @@
 # $Id$
 
-quantcut <- function(x, q=seq(0,1,by=0.25), na.rm=TRUE, ... )
+quantcut <- function(x, q=4, na.rm=TRUE, ... )
   {
+    if(length(q)==1)
+        q <- seq(0,1, length.out=q+1)
+    
     quant <- quantile(x, q, na.rm=na.rm)
     dups <- duplicated(quant)
     if(any(dups))

Modified: trunk/gtools/man/quantcut.Rd
===================================================================
--- trunk/gtools/man/quantcut.Rd	2015-04-23 21:23:36 UTC (rev 1948)
+++ trunk/gtools/man/quantcut.Rd	2015-04-23 21:47:48 UTC (rev 1949)
@@ -13,8 +13,10 @@
 %- maybe also `usage' for other objects documented here.
 \arguments{
   \item{x}{ Continous variable. }
-  \item{q}{ Vector of quantiles used for creating groups. Defaults to
-    \code{seq(0, 1, by=0.25)}.  See \code{\link{quantile}} for details. }
+  \item{q}{ Either a integer number of equally spaced quantile groups to
+    create, or a vector of quantiles used for creating groups. Defaults to
+    \code{q=4} which is equivalent to \code{q=seq(0, 1, by=0.25)}.
+    See \code{\link{quantile}} for details. }
   \item{na.rm}{ Boolean indicating whether missing values should be
     removed when computing quantiles.  Defaults to TRUE.}
   \item{\dots}{ Optional arguments passed to \code{\link{cut}}. }
@@ -31,7 +33,7 @@
   of quantile intervals.
 }
 \value{
-  Factor variable with one level for each quantile interval given by \code{q}.
+  Factor variable with one level for each quantile interval.
 }
 
 \author{Gregory R. Warnes \email{gr...@wa...}}
@@ -51,13 +53,19 @@
   table(quartiles)
 
   ## cut into deciles
-  deciles <- quantcut( x, seq(0,1,by=0.1) )
-  table(deciles)
+  deciles.1 <- quantcut( x, 10 )
+  table(deciles.1)
+  # or equivalently 
+  deciles.2 <- quantcut( x, seq(0,1,by=0.1) ) 
 
+  \testonly{
+    stopifnot(identical(deciles.1, deciles.2))
+  }
+
   ## show handling of 'tied' quantiles.
   x <- round(x)  # discretize to create ties
   stem(x)        # display the ties
-  deciles <- quantcut( x, seq(0,1,by=0.1) )
+  deciles <- quantcut( x, 10 )
 
   table(deciles) # note that there are only 5 groups (not 10) 
                  # due to duplicates

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1948] trunk/gplots/R/plotCI.R

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

Revision: 1948
          http://sourceforge.net/p/r-gregmisc/code/1948
Author:   warnes
Date:     2015-04-23 21:23:36 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
- plotCI() was not properly respecting the 'type=' argument.  This has
  been corrected.

Modified Paths:
--------------
    trunk/gplots/R/plotCI.R

Modified: trunk/gplots/R/plotCI.R
===================================================================
--- trunk/gplots/R/plotCI.R	2015-04-23 21:18:42 UTC (rev 1947)
+++ trunk/gplots/R/plotCI.R	2015-04-23 21:23:36 UTC (rev 1948)
@@ -103,7 +103,7 @@
     {
       if(invalid(labels) || labels==FALSE )
         plot(x, y, ylim = ylim, xlim=xlim, col=col,
-             xlab=xlab, ylab=ylab, ...)
+             xlab=xlab, ylab=ylab, type="n", ...)
       else
         {
           plot(x, y, ylim = ylim, xlim=xlim, col=col, type="n",

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1947] trunk/gplots/R/overplot.R

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

Revision: 1947
          http://sourceforge.net/p/r-gregmisc/code/1947
Author:   warnes
Date:     2015-04-23 21:18:42 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
- Remove stray browser() call from overplot()

Modified Paths:
--------------
    trunk/gplots/R/overplot.R

Modified: trunk/gplots/R/overplot.R
===================================================================
--- trunk/gplots/R/overplot.R	2015-04-23 21:10:33 UTC (rev 1946)
+++ trunk/gplots/R/overplot.R	2015-04-23 21:18:42 UTC (rev 1947)
@@ -58,8 +58,6 @@
   x.all.min <- min(x, na.rm=TRUE)
   x.all.max <- max(x, na.rm=TRUE)
 
-  if(y.all.min==y.all.max) browser()
-
   if (length(cond) == 0) {
     cond <- list(as.factor(rep(1, length(x))))
   }

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1946] trunk/gtools/DESCRIPTION

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

Revision: 1946
          http://sourceforge.net/p/r-gregmisc/code/1946
Author:   warnes
Date:     2015-04-23 21:10:33 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
Revers accidental text deletion:

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

Modified: trunk/gtools/DESCRIPTION
===================================================================
--- trunk/gtools/DESCRIPTION	2015-04-23 21:09:19 UTC (rev 1945)
+++ trunk/gtools/DESCRIPTION	2015-04-23 21:10:33 UTC (rev 1946)
@@ -1,3 +1,26 @@
+Package: gtools
+Title: Various R Programming Tools
+Description: Functions to assist in R programming, including:
+  - assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion', 
+    'getDependencies', 'keywords', 'scat'), 
+  - calculate the logit and inverse logit transformations ('logit', 'inv.logit'),
+  - test if a value is missing, empty or contains only NA and NULL values ('invalid'),
+  - manipulate R's .Last function ('addLast'),
+  - define macros ('defmacro'),
+  - detect odd and even integers ('odd', 'even'),
+  - convert strings containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy'), 
+  - perform a binary search ('binsearch'),
+  - sort strings containing both numeric and character components ('mixedsort'),
+  - create a factor variable from the quantiles of a continuous variable ('quantcut'),
+  - enumerate permutations and combinations ('combinations', 'permutation'),
+  - calculate and convert between fold-change and log-ratio ('foldchange', 
+    'logratio2foldchange', 'foldchange2logratio'),
+  - calculate probabilities and generate random numbers from Dirichlet distributions 
+    ('rdirichlet', 'ddirichlet'),
+  - apply a function over adjacent subsets of a vector ('running'),
+  - Modify the TCP\_NODELAY ('de-Nagle') flag for socket objects,
+  - Efficient 'rbind' of data frames, even if the column names don't match ('smartbind'),
+  - Generate significance stars from p-values ('stars.pval').
 Version: 3.4.3
 Date: 2015-04-23
 Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1945] trunk/gtools

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

Revision: 1945
          http://sourceforge.net/p/r-gregmisc/code/1945
Author:   warnes
Date:     2015-04-23 21:09:19 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
Update for gtools 3.4.3

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

Modified: trunk/gtools/DESCRIPTION
===================================================================
--- trunk/gtools/DESCRIPTION	2015-04-23 21:06:19 UTC (rev 1944)
+++ trunk/gtools/DESCRIPTION	2015-04-23 21:09:19 UTC (rev 1945)
@@ -1,28 +1,5 @@
-Package: gtools
-Title: Various R Programming Tools
-Description: Functions to assist in R programming, including:
-  - assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion', 
-    'getDependencies', 'keywords', 'scat'), 
-  - calculate the logit and inverse logit transformations ('logit', 'inv.logit'),
-  - test if a value is missing, empty or contains only NA and NULL values ('invalid'),
-  - manipulate R's .Last function ('addLast'),
-  - define macros ('defmacro'),
-  - detect odd and even integers ('odd', 'even'),
-  - convert strings containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy'), 
-  - perform a binary search ('binsearch'),
-  - sort strings containing both numeric and character components ('mixedsort'),
-  - create a factor variable from the quantiles of a continuous variable ('quantcut'),
-  - enumerate permutations and combinations ('combinations', 'permutation'),
-  - calculate and convert between fold-change and log-ratio ('foldchange', 
-    'logratio2foldchange', 'foldchange2logratio'),
-  - calculate probabilities and generate random numbers from Dirichlet distributions 
-    ('rdirichlet', 'ddirichlet'),
-  - apply a function over adjacent subsets of a vector ('running'),
-  - Modify the TCP\_NODELAY ('de-Nagle') flag for socket objects,
-  - Efficient 'rbind' of data frames, even if the column names don't match ('smartbind'),
-  - Generate significance stars from p-values ('stars.pval').
-Version: 3.4.2
-Date: 2015-04-06
+Version: 3.4.3
+Date: 2015-04-23
 Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
 Maintainer: Gregory R. Warnes <gr...@wa...>
 License: LGPL-2.1

Modified: trunk/gtools/inst/ChangeLog
===================================================================
--- trunk/gtools/inst/ChangeLog	2015-04-23 21:06:19 UTC (rev 1944)
+++ trunk/gtools/inst/ChangeLog	2015-04-23 21:09:19 UTC (rev 1945)
@@ -1,5 +1,15 @@
+2015-04-23  warnes
+
+	* [r1944] R/smartbind.R, R/strmacro.R: Remove debugging code and
+	  stray browser() call
+
+2015-04-14  warnes
+
+	* [r1923] DESCRIPTION: Fix typo
+
 2015-04-09  warnes
 
+	* [r1921] inst/ChangeLog: Update gtools ChangeLog
 	* [r1920] DESCRIPTION, NAMESPACE, R/loadedPackages.R,
 	  R/na.replace.R, inst/ChangeLog, inst/NEWS, man/loadedPackages.Rd,
 	  man/na.replace.Rd: Move first()/last()/left()/right() to gdata.

Modified: trunk/gtools/inst/NEWS
===================================================================
--- trunk/gtools/inst/NEWS	2015-04-23 21:06:19 UTC (rev 1944)
+++ trunk/gtools/inst/NEWS	2015-04-23 21:09:19 UTC (rev 1945)
@@ -1,3 +1,15 @@
+gtools 3.4.3 - 2015-04-06
+-------------------------
+
+Bug fixes:
+
+- Removed stray browser() call in smartbind().
+
+Other changes:
+
+- Correct typographical errors in package description.
+
+
 gtools 3.4.2 - 2015-04-06
 -------------------------
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1944] trunk/gtools/R

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

Revision: 1944
          http://sourceforge.net/p/r-gregmisc/code/1944
Author:   warnes
Date:     2015-04-23 21:06:19 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
Remove debugging code and stray browser() call

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

Modified: trunk/gtools/R/smartbind.R
===================================================================
--- trunk/gtools/R/smartbind.R	2015-04-23 20:21:21 UTC (rev 1943)
+++ trunk/gtools/R/smartbind.R	2015-04-23 21:06:19 UTC (rev 1944)
@@ -167,7 +167,6 @@
 
                 if(length(colClass)>1) # not just plain factor
                    {
-                     browser()
                     warning( "column '", col, "' of class ",
                             paste("'", colClass, "'", collapse=":",
                                   sep="'"),

Modified: trunk/gtools/R/strmacro.R
===================================================================
--- trunk/gtools/R/strmacro.R	2015-04-23 20:21:21 UTC (rev 1943)
+++ trunk/gtools/R/strmacro.R	2015-04-23 21:06:19 UTC (rev 1944)
@@ -22,11 +22,6 @@
         {
           a[[i]] <- a[[i]]
         }
-      #if (nn[i] == "DOTS")
-      #  {
-      #    nn[i] <- "..."
-      #    a[[i]] <- formals(function(...){})[[1]]
-      #  }
     }
   names(a) <- nn
   a <- as.list(a)
@@ -38,28 +33,12 @@
         ## build replacement list
         reptab <- a # copy defaults first
         reptab$"..." <- NULL
-        #reptab$DOTS <- ""
         
         args <- match.call(expand.dots=TRUE)[-1]
-        #print(args)
                           
         for(item in names(args))
-          ##if(item %in% names(reptab))
           reptab[[item]] <- args[[item]]
-        ##else
-        ##  {
-        ##    browser()
-        ##    oldval <- reptab[["DOTS"]]
-        ##    addval <- paste(item, "=", args[[item]])
-        ##    if(oldval>"")
-        ##      newval <- paste(c(oldval, addval), collapse=", ")
-        ##    else
-        ##      newval <- addval
-        ##    reptab[["DOTS"]] <- newval
-        ##  }
         
-        #print(reptab)
-        
         ## do the replacements
         body <- strexpr
         for(i in 1:length(reptab))
@@ -77,8 +56,6 @@
                          body)
           }
 
-        #print(body)
-        
         fun <- parse(text=body)
         eval(fun, parent.frame())
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1943] trunk/gplots/man/balloonplot.Rd

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

Revision: 1943
          http://sourceforge.net/p/r-gregmisc/code/1943
Author:   warnes
Date:     2015-04-23 20:21:21 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
Explicitly specify argument to gplots:::reorder.factor to prevent error.

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

Modified: trunk/gplots/man/balloonplot.Rd
===================================================================
--- trunk/gplots/man/balloonplot.Rd	2015-04-23 19:58:44 UTC (rev 1942)
+++ trunk/gplots/man/balloonplot.Rd	2015-04-23 20:21:21 UTC (rev 1943)
@@ -172,7 +172,8 @@
 
 balloonplot(x=list(Age,Sex),
             y=list(Class=Class,
-            Survived=gdata::reorder.factor(Survived,c(2,1))),
+                   Survived=gdata::reorder.factor(Survived,new.order=c(2,1))
+                   ),
             z=Freq,
             zlab="Number of Passengers",
             sort=TRUE,

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[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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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1941] trunk/gplots/R/heatmap.2.R

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

Revision: 1941
          http://sourceforge.net/p/r-gregmisc/code/1941
Author:   warnes
Date:     2015-04-23 19:09:17 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
Patch submitted by Ilia Kats:
- easily extract and plot subclusters from a big heatmap using the
  same colorkey, by passing a dendgrogram of the subcluster together
  with the full data matrix and, optionally, the breaks of the full
  heatmap in order to obtain the same color scaling. This is useful if
  one wants to plot several subclusters as different panels in a
  paper, but maintain consistent color coding.
- Improves the behavior of the color key axis labels, as they now
  honor par("cex") and par("cex.lab").

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

Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R	2015-04-23 18:49:23 UTC (rev 1940)
+++ trunk/gplots/R/heatmap.2.R	2015-04-23 19:09:17 UTC (rev 1941)
@@ -194,6 +194,8 @@
       rowInd <- order.dendrogram(ddr)
       if(length(rowInd)>nr || any(rowInd<1 | rowInd > nr ))
          stop("Rowv dendrogram doesn't match size of x")
+      if (length(rowInd) < nr)
+          nr <- length(rowInd)
     }
   else if (is.integer(Rowv))
     { ## Compute dendrogram and do reordering based on given vector
@@ -230,6 +232,8 @@
       colInd <- order.dendrogram(ddc)
       if(length(colInd)>nc || any(colInd<1 | colInd > nc ))
          stop("Colv dendrogram doesn't match size of x")
+      if (length(colInd) < nc)
+          nc <- length(colInd)
     }
   else if(identical(Colv, "Rowv")) {
     if(nr != nc)
@@ -633,8 +637,8 @@
         }
       else
         {
-          min.raw <- min(x, na.rm=TRUE) ## Again, modified to use scaled
-          max.raw <- max(x, na.rm=TRUE) ## or unscaled (SD 12/2/03)
+          min.raw <- min.breaks
+          max.raw <- max.breaks
         }
 
       z <- seq(min.raw, max.raw, length=length(col))
@@ -661,7 +665,7 @@
             key.xlab <- "Value"
       }
       if (!is.na(key.xlab)) {
-          mtext(side=1, key.xlab, line=par("mgp")[1], padj=0.5)
+          mtext(side=1, key.xlab, line=par("mgp")[1], padj=0.5, cex=par("cex") * par("cex.lab"))
       }
 
       if(density.info=="density")
@@ -687,7 +691,7 @@
           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)
+            mtext(side=2,key.ylab, line=par("mgp")[1], padj=0.5, cex=par("cex") * par("cex.lab"))
         }
       else if(density.info=="histogram")
         {
@@ -710,7 +714,7 @@
           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)
+            mtext(side=2,key.ylab, line=par("mgp")[1], padj=0.5, cex=par("cex") * par("cex.lab"))
         }
       else
           if (is.null(key.title))

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1940] trunk/gplots/R/heatmap.2.R

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

Revision: 1940
          http://sourceforge.net/p/r-gregmisc/code/1940
Author:   warnes
Date:     2015-04-23 18:49:23 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
In heatmap.2() split calls to distfun() and hclustfun() into separate steps to make debugging easier

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

Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R	2015-04-23 17:40:13 UTC (rev 1939)
+++ trunk/gplots/R/heatmap.2.R	2015-04-23 18:49:23 UTC (rev 1940)
@@ -198,7 +198,8 @@
   else if (is.integer(Rowv))
     { ## Compute dendrogram and do reordering based on given vector
         browser()
-      hcr <- hclustfun(distfun(x))
+      distr <- distfun(x)       
+      hcr <- hclustfun(distr)
       ddr <- as.dendrogram(hcr)
       ddr <- reorderfun(ddr, Rowv)
 
@@ -209,7 +210,8 @@
   else if (isTRUE(Rowv))
     { ## If TRUE, compute dendrogram and do reordering based on rowMeans
       Rowv <- rowMeans(x, na.rm = na.rm)
-      hcr <- hclustfun(distfun(x))
+      distr <- distfun(x)
+      hcr <- hclustfun(distr)
       ddr <- as.dendrogram(hcr)
       ddr <- reorderfun(ddr, Rowv)
 
@@ -240,7 +242,8 @@
     colInd <- rowInd
   } else if(is.integer(Colv))
     {## Compute dendrogram and do reordering based on given vector
-      hcc <- hclustfun(distfun(if(symm)x else t(x)))
+      distc <- distfun(if(symm)x else t(x))
+      hcc <- hclustfun(distc)
       ddc <- as.dendrogram(hcc)
       ddc <- reorderfun(ddc, Colv)
 
@@ -251,7 +254,8 @@
   else if (isTRUE(Colv))
     {## If TRUE, compute dendrogram and do reordering based on rowMeans
       Colv <- colMeans(x, na.rm = na.rm)
-      hcc <- hclustfun(distfun(if(symm)x else t(x)))
+      distc <- distfun(if(symm)x else t(x))
+      hcc <- hclustfun(distc)
       ddc <- as.dendrogram(hcc)
       ddc <- reorderfun(ddc, Colv)
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1939] trunk/gdata/inst

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

Revision: 1939
          http://sourceforge.net/p/r-gregmisc/code/1939
Author:   warnes
Date:     2015-04-23 17:40:13 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
Update NEWS and ChangeLog

Modified Paths:
--------------
    trunk/gdata/inst/ChangeLog
    trunk/gdata/inst/NEWS

Modified: trunk/gdata/inst/ChangeLog
===================================================================
--- trunk/gdata/inst/ChangeLog	2015-04-23 17:37:37 UTC (rev 1938)
+++ trunk/gdata/inst/ChangeLog	2015-04-23 17:40:13 UTC (rev 1939)
@@ -1,5 +1,12 @@
+2015-04-23  warnes
+
+	* [r1938] R/reorder.R: reorder.factor() now hands off processing to
+	  stats:::reorder.default() when either 'X' or 'FUN' is specified.
+
 2015-04-22  warnes
 
+	* [r1937] inst/ChangeLog, inst/NEWS: Update NEWS and ChangeLog for
+	  changes to humanReadable()
 	* [r1936] DESCRIPTION, R/humanReadable.R, R/object.size.R,
 	  man/humanReadable.Rd: Fix 'units' argument of humanReadable()
 	* [r1935] man/object.size.Rd: Update object.size() man page to

Modified: trunk/gdata/inst/NEWS
===================================================================
--- trunk/gdata/inst/NEWS	2015-04-23 17:37:37 UTC (rev 1938)
+++ trunk/gdata/inst/NEWS	2015-04-23 17:40:13 UTC (rev 1939)
@@ -26,8 +26,9 @@
 
 - reorder.factor() was ignoring the argument 'X', making it incompatible
   with the behavior of stats:::reorder.default(). This has been corrected,
-  and providing 'X' now returns the same results whether gdata is loaded 
-  or not.  (Reported by Sam Hunter.)
+  and providing either 'X' or 'FUN' causes processing to be handed off to 
+  stats:::reorder.defailt() so will return the same results whether gdata
+  is loaded or not.  (Reported by Sam Hunter.)
  
 Other changes:
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1938] trunk/gdata/R/reorder.R

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

Revision: 1938
          http://sourceforge.net/p/r-gregmisc/code/1938
Author:   warnes
Date:     2015-04-23 17:37:37 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
reorder.factor() now hands off processing to stats:::reorder.default() when either 'X' or 'FUN' is specified.

Modified Paths:
--------------
    trunk/gdata/R/reorder.R

Modified: trunk/gdata/R/reorder.R
===================================================================
--- trunk/gdata/R/reorder.R	2015-04-22 23:18:53 UTC (rev 1937)
+++ trunk/gdata/R/reorder.R	2015-04-23 17:37:37 UTC (rev 1938)
@@ -12,7 +12,7 @@
 {
     constructor <- if (order) ordered else factor
 
-    if(!missing(X))
+    if(!missing(X) || !missing(FUN))
        return( NextMethod(x)) 
 
     if (!missing(new.order))

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1937] trunk/gdata/inst

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

Revision: 1937
          http://sourceforge.net/p/r-gregmisc/code/1937
Author:   warnes
Date:     2015-04-22 23:18:53 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
Update NEWS and ChangeLog for changes to humanReadable()

Modified Paths:
--------------
    trunk/gdata/inst/ChangeLog
    trunk/gdata/inst/NEWS

Modified: trunk/gdata/inst/ChangeLog
===================================================================
--- trunk/gdata/inst/ChangeLog	2015-04-22 23:14:54 UTC (rev 1936)
+++ trunk/gdata/inst/ChangeLog	2015-04-22 23:18:53 UTC (rev 1937)
@@ -1,5 +1,12 @@
 2015-04-22  warnes
 
+	* [r1936] DESCRIPTION, R/humanReadable.R, R/object.size.R,
+	  man/humanReadable.Rd: Fix 'units' argument of humanReadable()
+	* [r1935] man/object.size.Rd: Update object.size() man page to
+	  reflect change in class of return value from 'object_size' to
+	  'object_sizes'
+	* [r1934] inst/ChangeLog, inst/NEWS: Update NEWS and ChangeLog for
+	  gdata 2.16.0
 	* [r1933] NAMESPACE, R/object.size.R: Modify gdaata:object.size to
 	  generate S3 objects of class 'object_sizes' (note the final 's')
 	  to avoid conflicts with methods in utils for object_size.

Modified: trunk/gdata/inst/NEWS
===================================================================
--- trunk/gdata/inst/NEWS	2015-04-22 23:14:54 UTC (rev 1936)
+++ trunk/gdata/inst/NEWS	2015-04-22 23:18:53 UTC (rev 1937)
@@ -13,6 +13,15 @@
   prevent numeric columns from being displayed using scientific
   notification.
 
+- The 'standard' argument to humanReadable() now accepts only two values,
+  'SI' for base 1000, and IEC for base 1024.
+
+- New 'units' argument to humanReadable() that permits specifying the
+  standard unit to use for all values.
+
+- The object.size() function now accepts the 'units' argument which is 
+  passed onto humanReadable().
+
 Bug fixes:
 
 - reorder.factor() was ignoring the argument 'X', making it incompatible

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1936] trunk/gdata

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

Revision: 1936
          http://sourceforge.net/p/r-gregmisc/code/1936
Author:   warnes
Date:     2015-04-22 23:14:54 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
Fix 'units' argument of humanReadable()

Modified Paths:
--------------
    trunk/gdata/DESCRIPTION
    trunk/gdata/R/object.size.R
    trunk/gdata/man/humanReadable.Rd

Added Paths:
-----------
    trunk/gdata/R/humanReadable.R

Modified: trunk/gdata/DESCRIPTION
===================================================================
--- trunk/gdata/DESCRIPTION	2015-04-22 22:44:46 UTC (rev 1935)
+++ trunk/gdata/DESCRIPTION	2015-04-22 23:14:54 UTC (rev 1936)
@@ -4,8 +4,8 @@
 Depends: R (>= 2.13.0)
 SystemRequirements: perl
 Imports: gtools
-Version: 2.15.0
-Date: 2015-04-06
+Version: 2.16.0
+Date: 2015-04-21
 Author: Gregory R. Warnes, Ben Bolker, Gregor Gorjanc, Gabor
         Grothendieck, Ales Korosec, Thomas Lumley, Don MacQueen, Arni
         Magnusson, Jim Rogers, and others

Added: trunk/gdata/R/humanReadable.R
===================================================================
--- trunk/gdata/R/humanReadable.R	                        (rev 0)
+++ trunk/gdata/R/humanReadable.R	2015-04-22 23:14:54 UTC (rev 1936)
@@ -0,0 +1,61 @@
+humanReadable <- function(x, standard=c("SI", "IEC"), units, digits=1, width=3, sep=" ")
+{
+  ## --- Setup ---
+
+  suffix.decimal <- c("B", "kB",  "MB",  "GB",  "TB",  "PB",  "EB",  "ZB",  "YB")
+  suffix.binary  <- c("B", "KiB", "MiB", "GiB", "TiB", "PiB", "EiB", "ZiB", "YiB")
+
+  standard <- match.arg(standard)
+  
+  ## --- Functions ---
+
+  .applyHuman <- function(x, base, suffix, digits, width, sep)
+  {
+    ## Which suffix should we use?
+    n <- length(suffix)
+    for(i in 1:n) {
+      if(x >= base) {
+        if(i < n) x <- x / base
+      } else {
+        break
+      }
+    }
+    ## Formatting
+    if(is.null(width)) { ## the same formatting for all
+      x <- format(round(x=x, digits=digits), nsmall=digits)
+    } else {             ## similar to ls, du, and df
+      lenX <- nchar(x)
+      if(lenX > width) {
+        digitsMy <- width - (lenX - (lenX - (nchar(round(x)) + 1)))
+        digits <- ifelse(digitsMy > digits, digits, digitsMy)
+      }
+      if(i == 1) digits <- 0
+      x <- round(x, digits=digits)
+    }
+    paste(x, suffix[i], sep=sep)
+  }
+
+  ## -- Work
+  
+  if(any(x < 0)) stop("'x' must be positive")
+  if(standard == "SI") {
+    suffix <- suffix.decimal
+    base <- 10^3
+  } else {
+    suffix <- suffix.binary
+    base <- 2^10
+  }
+
+  if(!missing(units))
+      {
+          units <- match.arg( units, suffix )
+          power <- match(units, suffix ) -1
+          X <- x/(base^power)
+          X <- format.default(round(x=X, digits=digits), nsmall=digits)
+          X <- paste(X, units)
+          X
+      }
+  else
+      sapply(X=x, FUN=".applyHuman", base=base, suffix=suffix, digits=digits,
+             width=width, sep=sep)
+}

Modified: trunk/gdata/R/object.size.R
===================================================================
--- trunk/gdata/R/object.size.R	2015-04-22 22:44:46 UTC (rev 1935)
+++ trunk/gdata/R/object.size.R	2015-04-22 23:14:54 UTC (rev 1936)
@@ -104,5 +104,6 @@
              width=width, sep=sep)
 }
 
+
 ###------------------------------------------------------------------------
 ### object.size.R ends here

Modified: trunk/gdata/man/humanReadable.Rd
===================================================================
--- trunk/gdata/man/humanReadable.Rd	2015-04-22 22:44:46 UTC (rev 1935)
+++ trunk/gdata/man/humanReadable.Rd	2015-04-22 23:14:54 UTC (rev 1936)
@@ -19,15 +19,14 @@
 }
 
 \usage{
-
-humanReadable(x, standard="SI", digits=1, width=3, sep=" ")
-
+humanReadable(x, standard=c("SI","IEC"), units, digits=1, width=3, sep=" ")
 }
 
 \arguments{
   \item{x}{integer, byte size}
-  \item{standard}{character, "SI" for powers of 1000 or anything else for
+  \item{standard}{character, either "SI" for powers of 1000 or "IEC" for
     powers of 1024, see details}
+  \item{units}{character, unit to use for all values (optional)}
   \item{digits}{integer, number of digits after decimal point}
   \item{width}{integer, width of number string}
   \item{sep}{character, separator between number and unit}
@@ -104,6 +103,14 @@
 
 \examples{
 
+# Simple example: maximum addressible size of 32 bit pointer
+humanReadable(2^32-1, standard="SI")
+humanReadable(2^32-1, standard="IEC")
+
+humanReadable(2^32-1, standard="SI",  unit="MB")
+humanReadable(2^32-1, standard="IEC", unit="MiB")
+
+
 baseSI <- 10
 powerSI <- seq(from=3, to=27, by=3)
 SI0 <- (baseSI)^powerSI
@@ -117,12 +124,22 @@
 IEC1 <- IEC0 - IEC0 / c(2, runif(n=k, min=1.01, max=5.99))
 IEC2 <- IEC0 + IEC0 / c(2, runif(n=k, min=1.01, max=5.99))
 
+# Auto units
 cbind(humanReadable(x=SI1, width=NULL, digits=3),
       humanReadable(x=SI0, width=NULL, digits=2),
       humanReadable(x=SI2, width=NULL, digits=1),
       humanReadable(x=IEC1, standard="IEC", width=7, digits=3),
       humanReadable(x=IEC0, standard="IEC", width=7, digits=2),
       humanReadable(x=IEC2, standard="IEC", width=7, digits=1))
+
+# Single unit
+cbind(humanReadable(x=SI1, units="GB", width=NULL, digits=3),
+      humanReadable(x=SI0, units="GB", width=NULL, digits=2),
+      humanReadable(x=SI2, units="GB", width=NULL, digits=1),
+      humanReadable(x=IEC1, units="GiB", standard="IEC", width=7, digits=3),
+      humanReadable(x=IEC0, units="GiB", standard="IEC", width=7, digits=2),
+      humanReadable(x=IEC2, units="GiB", standard="IEC", width=7, digits=1))
+
 }
 
 \keyword{misc}

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1935] trunk/gdata/man/object.size.Rd

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

Revision: 1935
          http://sourceforge.net/p/r-gregmisc/code/1935
Author:   warnes
Date:     2015-04-22 22:44:46 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
Update object.size() man page to reflect change in class of return value from 'object_size' to 'object_sizes'

Modified Paths:
--------------
    trunk/gdata/man/object.size.Rd

Modified: trunk/gdata/man/object.size.Rd
===================================================================
--- trunk/gdata/man/object.size.Rd	2015-04-22 22:41:58 UTC (rev 1934)
+++ trunk/gdata/man/object.size.Rd	2015-04-22 22:44:46 UTC (rev 1935)
@@ -5,10 +5,10 @@
 
 \name{object.size}
 \alias{object.size}
-\alias{print.object_size}
-\alias{c.object_size}
-\alias{as.object_size}
-\alias{is.object_size}
+\alias{print.object_sizes}
+\alias{c.object_sizes}
+\alias{as.object_sizes}
+\alias{is.object_sizes}
 
 \title{Report the Space Allocated for an Object}
 \description{
@@ -17,7 +17,7 @@
 \usage{
 object.size(\dots)
 
-\method{print}{object_size}(x, quote=FALSE, humanReadable, \dots)
+\method{print}{object_sizes}(x, quote=FALSE, humanReadable, \dots)
 }
 \arguments{
   \item{\dots}{\code{object.size}: \R objects; \code{print}; arguments 
@@ -76,10 +76,10 @@
             object.size(get(x, envir = baseenv())))
 (tmp <- as.matrix(rev(sort(z))[1:10]))
 
-as.object_size(14567567)
+as.object_sizes(14567567)
 options(humanReadable=TRUE)
 (z <- object.size(letters, c(letters, letters), rep(letters, 100), rep(letters, 10000)))
-is.object_size(z)
-as.object_size(14567567)
+is.object_sizes(z)
+as.object_sizes(14567567)
 }
 \keyword{utilities}

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1934] trunk/gdata/inst

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

Revision: 1934
          http://sourceforge.net/p/r-gregmisc/code/1934
Author:   warnes
Date:     2015-04-22 22:41:58 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
Update NEWS and ChangeLog for gdata 2.16.0

Modified Paths:
--------------
    trunk/gdata/inst/ChangeLog
    trunk/gdata/inst/NEWS

Modified: trunk/gdata/inst/ChangeLog
===================================================================
--- trunk/gdata/inst/ChangeLog	2015-04-22 22:34:53 UTC (rev 1933)
+++ trunk/gdata/inst/ChangeLog	2015-04-22 22:41:58 UTC (rev 1934)
@@ -1,5 +1,16 @@
+2015-04-22  warnes
+
+	* [r1933] NAMESPACE, R/object.size.R: Modify gdaata:object.size to
+	  generate S3 objects of class 'object_sizes' (note the final 's')
+	  to avoid conflicts with methods in utils for object_size.
+	* [r1932] R/reorder.R, tests/test.reorder.factor.R,
+	  tests/test.reorder.factor.Rout.save: Correct behavior of
+	  reorder.factor() when argument 'X' is supplied by delgating to
+	  stats:::reorder.default()
+
 2015-04-14  warnes
 
+	* [r1929] inst/ChangeLog: Update ChangeLog
 	* [r1928] man/write.fwf.Rd: Remove editorializing
 	* [r1927] inst/ChangeLog, inst/NEWS: Update NEWS and ChangeLog for
 	  gdata 2.15.0

Modified: trunk/gdata/inst/NEWS
===================================================================
--- trunk/gdata/inst/NEWS	2015-04-22 22:34:53 UTC (rev 1933)
+++ trunk/gdata/inst/NEWS	2015-04-22 22:41:58 UTC (rev 1934)
@@ -1,4 +1,4 @@
-Changes in 2.15.0 (2015-04-06)
+Changes in 2.16.0 (2015-04-21)
 ------------------------------
 
 New features:
@@ -13,12 +13,23 @@
   prevent numeric columns from being displayed using scientific
   notification.
 
+Bug fixes:
+
+- reorder.factor() was ignoring the argument 'X', making it incompatible
+  with the behavior of stats:::reorder.default(). This has been corrected,
+  and providing 'X' now returns the same results whether gdata is loaded 
+  or not.  (Reported by Sam Hunter.)
+ 
 Other changes:
 
-- Replaced depricated PERL function POSIX::isdigit with equivalent
-  regular expression.
+- Replaced depricated PERL function POSIX::isdigit with equivalent regular 
+  expression.
 
+- object.size() now returns objects with S3 class 'object_sizes' (note the 
+  final 's') to avoid conflicts with methods in utils for class 'object_size' 
+  which can only handle a scalar size.
 
+
 Changes in 2.14.0 (2014-08-27)
 ------------------------------
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1933] trunk/gdata

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

Revision: 1933
          http://sourceforge.net/p/r-gregmisc/code/1933
Author:   warnes
Date:     2015-04-22 22:34:53 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
Modify gdaata:object.size to generate S3 objects of class 'object_sizes' (note the final 's') to avoid conflicts with methods in utils for object_size.

Modified Paths:
--------------
    trunk/gdata/NAMESPACE
    trunk/gdata/R/object.size.R

Modified: trunk/gdata/NAMESPACE
===================================================================
--- trunk/gdata/NAMESPACE	2015-04-22 22:32:01 UTC (rev 1932)
+++ trunk/gdata/NAMESPACE	2015-04-22 22:34:53 UTC (rev 1933)
@@ -52,7 +52,7 @@
        xlsFormats,
 
        ## Object size stuff
-       object.size, as.object_size, is.object_size, humanReadable,
+       object.size, as.object_sizes, is.object_sizes, humanReadable,
 
        ## getDateTime stuff
        getYear, getMonth, getDay, getHour, getMin, getSec,
@@ -129,8 +129,8 @@
 S3method(nobs, lm)      # now provided by stats package
 
 ## Object size stuff
-S3method(print, object_size)
-S3method(c, object_size)
+S3method(print, object_sizes)
+S3method(c, object_sizes)
 
 ## unknown stuff
 S3method(isUnknown, default)

Modified: trunk/gdata/R/object.size.R
===================================================================
--- trunk/gdata/R/object.size.R	2015-04-22 22:32:01 UTC (rev 1932)
+++ trunk/gdata/R/object.size.R	2015-04-22 22:34:53 UTC (rev 1933)
@@ -4,15 +4,15 @@
 ### $Id$
 ### Time-stamp: <2008-12-30 08:05:43 ggorjan>
 ###------------------------------------------------------------------------
-
 object.size <- function(...) 
 {
   structure(sapply(list(...),
                    utils::object.size),
-                   class=c("object_size", "numeric"))
+                   class=c("object_sizes", "numeric"))
 }
 
-print.object_size <- function(x, quote=FALSE, humanReadable, ...)
+print.object_sizes <- function(x, quote=FALSE, units,
+                                  humanReadable, ...)
 {  
   xOrig <- x
   if(missing(humanReadable)) {
@@ -28,37 +28,31 @@
   invisible(xOrig)
 }
 
-is.object_size <- function(x) inherits(x, what="object_size")
+is.object_sizes <- function(x) inherits(x, what="object_sizes")
    
-as.object_size <- function(x)
+as.object_sizes <- function(x)
 {
   if(!is.numeric(x)) stop("'x' must be numeric/integer")
-  class(x) <- c("object_size", "numeric")
+  class(x) <- c("object_sizes", "numeric")
   x
 }
 
-c.object_size <- function(..., recursive=FALSE)
+c.object_sizes <- function(..., recursive=FALSE)
 {
   x <- NextMethod()
-  if(is.numeric(x)) class(x) <- c("object_size", "numeric")
+  if(is.numeric(x)) class(x) <- c("object_sizes", "numeric")
   x
 }
 
-humanReadable <- function(x, standard="SI", digits=1, width=3, sep=" ")
+humanReadable <- function(x, standard="SI", units, digits=1, width=3, sep=" ")
 {
   ## --- Setup ---
 
-  if(any(x < 0)) stop("'x' must be positive")
-  if(standard == "SI") {
-    suffix <- c("B", "kB",  "MB",  "GB",  "TB",  "PB",  "EB",  "ZB",  "YB")
-    base <- 1000
-  } else {
-    suffix <- c("B", "KiB", "MiB", "GiB", "TiB", "PiB", "EiB", "ZiB", "YiB")
-    base <- 1024
-  }
+  suffix.decimal <- c("B", "kB",  "MB",  "GB",  "TB",  "PB",  "EB",  "ZB",  "YB")
+  suffix.binary  <- c("B", "KiB", "MiB", "GiB", "TiB", "PiB", "EiB", "ZiB", "YiB")
+    
+  ## --- Functions ---
 
-  ## --- Apply ---
-
   .applyHuman <- function(x, base, suffix, digits, width, sep)
   {
     ## Which suffix should we use?
@@ -85,8 +79,29 @@
     paste(x, suffix[i], sep=sep)
   }
 
-  sapply(X=x, FUN=".applyHuman", base=base, suffix=suffix, digits=digits,
-         width=width, sep=sep)
+  ## -- Work
+  
+  if(any(x < 0)) stop("'x' must be positive")
+  if(standard == "SI") {
+    suffix <- suffix.decimal
+    base <- 10^3
+  } else {
+    suffix <- suffix.binary
+    base <- 2^10
+  }
+
+  if(!missing(units))
+      {
+          units <- match.arg( units, suffix )
+          power <- which( units %in% suffix ) -1
+          X <- x/(base^power)
+          X <- format.default(round(x=x, digits=digits), nsmall=digits)
+          X <- paste(X, units)
+          X
+      }
+  else
+      sapply(X=x, FUN=".applyHuman", base=base, suffix=suffix, digits=digits,
+             width=width, sep=sep)
 }
 
 ###------------------------------------------------------------------------

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1932] trunk/gdata

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

Revision: 1932
          http://sourceforge.net/p/r-gregmisc/code/1932
Author:   warnes
Date:     2015-04-22 22:32:01 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
Correct behavior of reorder.factor() when argument 'X' is supplied by delgating to stats:::reorder.default()

Modified Paths:
--------------
    trunk/gdata/R/reorder.R

Added Paths:
-----------
    trunk/gdata/tests/test.reorder.factor.R
    trunk/gdata/tests/test.reorder.factor.Rout.save

Modified: trunk/gdata/R/reorder.R
===================================================================
--- trunk/gdata/R/reorder.R	2015-04-22 21:35:19 UTC (rev 1931)
+++ trunk/gdata/R/reorder.R	2015-04-22 22:32:01 UTC (rev 1932)
@@ -12,6 +12,9 @@
 {
     constructor <- if (order) ordered else factor
 
+    if(!missing(X))
+       return( NextMethod(x)) 
+
     if (!missing(new.order))
       {
         if (is.numeric(new.order))

Added: trunk/gdata/tests/test.reorder.factor.R
===================================================================
--- trunk/gdata/tests/test.reorder.factor.R	                        (rev 0)
+++ trunk/gdata/tests/test.reorder.factor.R	2015-04-22 22:32:01 UTC (rev 1932)
@@ -0,0 +1,11 @@
+## Test results before and after loading gdata
+
+m <- factor(c('a','b','c'))
+
+( m1 <- reorder(m, X=c(3, 2, 1)) )
+
+library(gdata)
+
+( m2 <- reorder(m, X=c(3, 2, 1)) )
+
+stopifnot(identical(m1,m2))

Added: trunk/gdata/tests/test.reorder.factor.Rout.save
===================================================================
--- trunk/gdata/tests/test.reorder.factor.Rout.save	                        (rev 0)
+++ trunk/gdata/tests/test.reorder.factor.Rout.save	2015-04-22 22:32:01 UTC (rev 1932)
@@ -0,0 +1,60 @@
+
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+  Natural language support but running in an English locale
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> ## Test results before and after loading gdata
+> 
+> m <- factor(c('a','b','c'))
+> 
+> ( m1 <- reorder(m, X=c(3, 2, 1)) )
+[1] a b c
+attr(,"scores")
+a b c 
+3 2 1 
+Levels: c b a
+> 
+> library(gdata)
+gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
+
+gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
+
+Attaching package: ‘gdata’
+
+The following object is masked from ‘package:stats’:
+
+    nobs
+
+The following object is masked from ‘package:utils’:
+
+    object.size
+
+Warning message:
+S3 methods ‘print.object_size’, ‘c.object_size’ were declared in NAMESPACE but not found 
+> 
+> ( m2 <- reorder(m, X=c(3, 2, 1)) )
+[1] a b c
+attr(,"scores")
+a b c 
+3 2 1 
+Levels: c b a
+> 
+> stopifnot(identical(m1,m2))
+> 
+> proc.time()
+   user  system elapsed 
+  0.512   0.070   0.638 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1931] trunk/gplots

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

Revision: 1931
          http://sourceforge.net/p/r-gregmisc/code/1931
Author:   warnes
Date:     2015-04-22 21:35:19 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
Update DESCRIPTION, ChangeLog, and NEWS for gplots 2.17.0

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

Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION	2015-04-22 21:33:06 UTC (rev 1930)
+++ trunk/gplots/DESCRIPTION	2015-04-22 21:35:19 UTC (rev 1931)
@@ -4,8 +4,8 @@
 Depends: R (>= 3.0)
 Imports: gtools, gdata, stats, caTools, KernSmooth
 Suggests: grid, MASS
-Version: 2.16.0
-Date: 2015-01-02
+Version: 2.17.0
+Date: 2015-04-21
 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/ChangeLog
===================================================================
--- trunk/gplots/inst/ChangeLog	2015-04-22 21:33:06 UTC (rev 1930)
+++ trunk/gplots/inst/ChangeLog	2015-04-22 21:35:19 UTC (rev 1931)
@@ -1,3 +1,33 @@
+2015-04-22  warnes
+
+	* [r1930] R/heatmap.2.R, man/heatmap.2.Rd: heatmap.2: add new
+	  'colRow' and 'colCol' arguments to control the color of row and
+	  column text labels
+
+2015-04-06  warnes
+
+	* [r1916] inst/ChangeLog: Add ChangeLog files to repository
+
+2015-01-02  warnes
+
+	* [r1913] DESCRIPTION, inst/NEWS: Update for gplots release 2.16.0.
+	* [r1912] R/plotmeans.R: Change default group count lable back to
+	  'n='.
+	* [r1911] R/plotmeans.R, man/plotmeans.Rd: - plotmeans: Pass
+	  optional graphical arguments captured in '...' axis function
+	  used to draw the x axis.
+	  - plotmeans: Add an new argument 'text.n.label' to specify the
+	  text
+	  used for labelingthe number of elements in a group.
+	* [r1910] R/plotmeans.R: - Remove S-Plus-specific code
+	  - Simplify model frame code
+
+2014-12-03  warnes
+
+	* [r1909] tests/heatmap2Test.Rout.save: Update stored test output
+	  to account for new startup message from KernSmooth package
+	* [r1908] DESCRIPTION: Fix package title capitalization.
+
 2014-12-02  warnes
 
 	* [r1907] inst/NEWS: Add descrioption of node stack overflow issue

Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS	2015-04-22 21:33:06 UTC (rev 1930)
+++ trunk/gplots/inst/NEWS	2015-04-22 21:35:19 UTC (rev 1931)
@@ -1,3 +1,12 @@
+Release 2.17.0 - 2015-04-21
+---------------------------
+
+New Features:
+
+- heatmap.2() has two new arguments, 'colRow' and 'colCol' to control
+  the color of row and column text labels.
+
+
 Release 2.16.0 - 2015-01-02
 ---------------------------
 

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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1930] trunk/gplots

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

Revision: 1930
          http://sourceforge.net/p/r-gregmisc/code/1930
Author:   warnes
Date:     2015-04-22 21:33:06 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
heatmap.2: add new 'colRow' and 'colCol' arguments to control the color of row and column text labels

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

Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R	2015-04-14 22:02:42 UTC (rev 1929)
+++ trunk/gplots/R/heatmap.2.R	2015-04-22 21:33:06 UTC (rev 1930)
@@ -59,6 +59,8 @@
                        adjCol = c(NA,0),
                        offsetRow = 0.5,
                        offsetCol = 0.5,
+                       colRow = NULL,
+                       colCol = NULL,
 
                        ## color key + density info
                        key = TRUE,
@@ -281,6 +283,12 @@
     labCol <- if(is.null(colnames(x))) (1:nc)[colInd] else colnames(x)
   else
     labCol <- labCol[colInd]
+  
+  if(!is.null(colRow))
+    colRow <- colRow[rowInd]
+  
+  if(!is.null(colCol))
+    colCol <- colCol[colInd]
 
   if(scale == "row") {
     retval$rowMeans <- rm <- rowMeans(x, na.rm = na.rm)
@@ -415,7 +423,7 @@
     }
 
   ## add column labels
-  if(is.null(srtCol))
+  if(is.null(srtCol) && is.null(colCol))
     axis(1,
          1:nc,
          labels= labCol,
@@ -428,7 +436,7 @@
          )
   else
     {
-      if(is.numeric(srtCol))
+      if(is.null(srtCol) || is.numeric(srtCol))
         {
           if(missing(adjCol) || is.null(adjCol))
             adjCol=c(1,NA)
@@ -442,7 +450,10 @@
                ##pos=1,
                adj=adjCol,
                cex=cexCol,
-               srt=srtCol)
+               srt=srtCol,
+               col=colCol
+               )
+          print(colCol)
           par(xpd=xpd.orig)
         }
       else
@@ -450,7 +461,7 @@
     }
 
   ## add row labels
-  if(is.null(srtRow))
+  if(is.null(srtRow) && is.null(colRow))
     {
       axis(4,
            iy,
@@ -465,7 +476,7 @@
     }
   else
     {
-      if(is.numeric(srtRow))
+      if(is.null(srtRow) || is.numeric(srtRow))
         {
           xpd.orig <- par("xpd")
           par(xpd=NA)
@@ -475,7 +486,8 @@
                labels=labRow,
                adj=adjRow,
                cex=cexRow,
-               srt=srtRow
+               srt=srtRow,
+               col=colRow
                )
           par(xpd=xpd.orig)
         }

Modified: trunk/gplots/man/heatmap.2.Rd
===================================================================
--- trunk/gplots/man/heatmap.2.Rd	2015-04-14 22:02:42 UTC (rev 1929)
+++ trunk/gplots/man/heatmap.2.Rd	2015-04-22 21:33:06 UTC (rev 1930)
@@ -71,6 +71,8 @@
            adjCol = c(NA,0),
            offsetRow = 0.5,
            offsetCol = 0.5,
+           colRow = NULL,
+           colCol = NULL,
 
            # color key + density info
            key = TRUE,
@@ -111,10 +113,11 @@
     \code{\link{dendrogram}}, then it is used "as-is", ie
     without any reordering. If a vector of integers, then dendrogram is
     computed and reordered based on the order of the vector.}
-  \item{Colv}{determines if and how the \emph{column} dendrogram should be
-    reordered.	Has the options as the \code{Rowv} argument above and
-    \emph{additionally} when \code{x} is a square matrix, \code{Colv =
-      "Rowv"} means that columns should be treated identically to the rows.}
+  \item{Colv}{determines if and how the \emph{column} dendrogram should
+    be reordered.	Has the options as the \code{Rowv} argument above and
+    \emph{additionally} when \code{x} is a square matrix, 
+    \code{Colv="Rowv"} means that columns should be treated identically
+    to the rows.}
   \item{distfun}{function used to compute the distance (dissimilarity)
     between both rows and columns.  Defaults to \code{\link{dist}}.}
   \item{hclustfun}{function used to compute the hierarchical clustering
@@ -128,7 +131,8 @@
     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.}
+    \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
@@ -150,12 +154,14 @@
   \item{col}{colors used for the image. Defaults to heat colors
     (\code{heat.colors}).}
   % block separation
-  \item{colsep, rowsep, sepcolor}{(optional) vector of integers indicating
-    which columns or rows should be separated from the preceding columns
-    or rows by a narrow space of color \code{sepcolor}.}
-  \item{sepwidth}{(optional)  Vector of length 2 giving the width (colsep) or height (rowsep) the separator box
-   drawn by colsep and rowsep as a function of the width (colsep) or
-   height (rowsep) of a cell. Defaults to \code{c(0.05, 0.05)}}
+  \item{colsep, rowsep, sepcolor}{(optional) vector of integers 
+    indicating which columns or rows should be separated from the
+    preceding columns or rows by a narrow space of color
+    \code{sepcolor}.}
+  \item{sepwidth}{(optional) Vector of length 2 giving the width
+    (colsep) or height (rowsep) the separator box drawn by colsep and
+    rowsep as a function of the width (colsep) or height (rowsep) of a
+    cell. Defaults to \code{c(0.05, 0.05)}}
   % cell labeling
   \item{cellnote}{(optional) matrix of character strings which will be
     placed within each color cell, e.g. p-value symbols.}
@@ -181,25 +187,31 @@
     defaults to the value of \code{tracecol}.}
   % Row/Column Labeling
   \item{margins}{numeric vector of length 2 containing the margins
-    (see \code{\link{par}(mar= *)}) for column and row names, respectively.}
-  \item{ColSideColors}{(optional) character vector of length \code{ncol(x)}
-    containing the color names for a horizontal side bar that may be used to
-    annotate the columns of \code{x}.}
-  \item{RowSideColors}{(optional) character vector of length \code{nrow(x)}
-    containing the color names for a vertical side bar that may be used to
-    annotate the rows of \code{x}.}
+    (see \code{\link{par}(mar= *)}) for column and row names, 
+    respectively.}
+  \item{ColSideColors}{(optional) character vector of length 
+    \code{ncol(x)} containing the color names for a horizontal side bar
+    that may be used to annotate the columns of \code{x}.}
+  \item{RowSideColors}{(optional) character vector of length 
+    \code{nrow(x)} containing the color names for a vertical side bar
+    that may be used to annotate the rows of \code{x}.}
   \item{cexRow, cexCol}{positive numbers, used as \code{cex.axis} in
     for the row or column axis labeling.  The defaults currently only
     use number of rows or columns, respectively.}
   \item{labRow, labCol}{character vectors with row and column labels to
     use; these default to \code{rownames(x)} or \code{colnames(x)},
     respectively.}
-  \item{srtRow, srtCol}{angle of row/column labels, in degrees from horizontal}
+  \item{srtRow, srtCol}{angle of row/column labels, in degrees from
+    horizontal}
   \item{adjRow, adjCol}{2-element vector giving the (left-right,
     top-bottom) justification of row/column labels (relative to the text
-           orientation).}
-  \item{offsetRow, offsetCol}{Number of character-width spaces to place
-           between row/column labels and the edge of the plotting region.}
+    orientation).}
+  \item{offsetRow, offsetCol}{Number of character-width spaces to 
+    place between row/column labels and the edge of the plotting 
+    region.}
+  \item{colRow, colCol}{color of row/column labels, either a scalar to
+    set the color of all labels the same, or a vector providing the
+    colors of each label item}
   % Color key and density info
   \item{key}{logical indicating whether a color-key should be shown.}
   \item{keysize}{numeric value indicating the size of the key}
@@ -226,8 +238,8 @@
     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.}
+    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
@@ -446,14 +458,19 @@
 	       RowSideColors=rc, ColSideColors=cc, margin=c(5, 10),
 	       xlab="specification variables", ylab= "Car Models",
 	       main="heatmap(<Mtcars data>, ..., scale=\"column\")",
-               tracecol="green", density="density")
+         tracecol="green", density="density")
  ## Note that the breakpoints are now symmetric about 0
+ 
+ ## Color the labels to match RowSideColors and ColSideColors
+ hv <- heatmap.2(x, col=cm.colors(255), scale="column",
+         RowSideColors=rc, ColSideColors=cc, margin=c(5, 10),
+	       xlab="specification variables", ylab= "Car Models",
+	       main="heatmap(<Mtcars data>, ..., scale=\"column\")",
+         tracecol="green", density="density", colRow=rc, colCol=cc,
+         srtCol=45, adjCol=c(0.5,1))
+ 
 
 
-
-
-
-
 %% want example using the `add.exp' argument!
 
  data(attitude)

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