[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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