[R-gregmisc-users] SF.net SVN: r-gregmisc:[1887] trunk/gplots

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

Revision: 1887
          http://sourceforge.net/p/r-gregmisc/code/1887
Author:   warnes
Date:     2014-09-16 18:08:39 +0000 (Tue, 16 Sep 2014)
Log Message:
-----------
- Correct statement of default color for 'notecol' argumemt to 'heatmap.2'.
- Modify default arguments to 'symbreaks' and 'symkey' to make the
  logic more evident by replacing min() with any().  (The previous
  code executed properly, but relied on implicit coercion of logicals
  to numeric, obscuring the intent.)

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	2014-09-13 01:17:27 UTC (rev 1886)
+++ trunk/gplots/R/heatmap.2.R	2014-09-16 18:08:39 UTC (rev 1887)
@@ -21,7 +21,7 @@
 
                        ## mapping data to colors
                        breaks,
-                       symbreaks=min(x < 0, na.rm=TRUE) || scale!="none",
+                       symbreaks=any(x < 0, na.rm=TRUE) || scale!="none",
 
                        ## colors
                        col="heat.colors",
@@ -65,7 +65,7 @@
                        keysize = 1.5,
                        density.info=c("histogram","density","none"),
                        denscol=tracecol,
-                       symkey = min(x < 0, na.rm=TRUE) || symbreaks,
+                       symkey = any(x < 0, na.rm=TRUE) || symbreaks,
                        densadj = 0.25,
                        key.title = NULL,
                        key.xlab = NULL,
@@ -555,7 +555,7 @@
 
   if( dendrogram %in% c("both","column") )
     {
-      plot(ddc, axes = FALSE, xaxs = "i", leaflab = "none")
+      plot.dendrogram(ddc, axes = FALSE, xaxs = "i", leaflab = "none")
     }
   else
     plot.new()

Modified: trunk/gplots/man/heatmap.2.Rd
===================================================================
--- trunk/gplots/man/heatmap.2.Rd	2014-09-13 01:17:27 UTC (rev 1886)
+++ trunk/gplots/man/heatmap.2.Rd	2014-09-16 18:08:39 UTC (rev 1887)
@@ -33,7 +33,7 @@
 
            # mapping data to colors
            breaks,
-           symbreaks=min(x < 0, na.rm=TRUE) || scale!="none",
+           symbreaks=any(x < 0, na.rm=TRUE) || scale!="none",
 
            # colors
            col="heat.colors",
@@ -77,7 +77,7 @@
            keysize = 1.5,
            density.info=c("histogram","density","none"),
            denscol=tracecol,
-           symkey = min(x < 0, na.rm=TRUE) || symbreaks,
+           symkey = any(x < 0, na.rm=TRUE) || symbreaks,
            densadj = 0.25,
            key.title = NULL,
            key.xlab = NULL,
@@ -126,7 +126,7 @@
     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}}.
+    \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
@@ -162,7 +162,7 @@
   \item{notecex}{(optional) numeric scaling factor for \code{cellnote}
     items.}
   \item{notecol}{(optional) character string specifying the color for
-    \code{cellnote} text.  Defaults to "green".}
+    \code{cellnote} text.  Defaults to "cyan".}
   \item{na.color}{Color to use for missing value (\code{NA}). Defaults
     to the plot background color.}
   % level trace

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