[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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