[R-gregmisc-users] SF.net SVN: r-gregmisc: [1252] trunk/gplots

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

Revision: 1252
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1252&view=rev
Author:   warnes
Date:     2008-04-07 09:47:30 -0700 (Mon, 07 Apr 2008)

Log Message:
-----------
Add ability to control location of individual heatmap.2 components

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	2008-03-27 22:36:13 UTC (rev 1251)
+++ trunk/gplots/R/heatmap.2.R	2008-04-07 16:47:30 UTC (rev 1252)
@@ -62,6 +62,11 @@
                      xlab = NULL,
                      ylab = NULL,
 
+                     # plot layout
+                     lmat = NULL,
+                     lhei = NULL,
+                     lwid = NULL,
+
                      # extras
                      ...
                      )
@@ -270,23 +275,45 @@
     x[] <- ifelse(x<min.breaks, min.breaks, x)
     x[] <- ifelse(x>max.breaks, max.breaks, x)
 
+
+
+  
+
+  
     ## Calculate the plot layout
-    lmat <- rbind(4:3, 2:1)
-    lhei <- lwid <- c(keysize, 4)
-    if(!missing(ColSideColors)) { ## add middle row to layout
-	if(!is.character(ColSideColors) || length(ColSideColors) != nc)
-	    stop("'ColSideColors' must be a character vector of length ncol(x)")
-	lmat <- rbind(lmat[1,]+1, c(NA,1), lmat[2,]+1)
-	lhei <- c(lhei[1], 0.2, lhei[2])
-    }
-    if(!missing(RowSideColors)) { ## add middle column to layout
-	if(!is.character(RowSideColors) || length(RowSideColors) != nr)
-	    stop("'RowSideColors' must be a character vector of length nrow(x)")
-	lmat <- cbind(lmat[,1]+1, c(rep(NA, nrow(lmat)-1), 1), lmat[,2]+1)
-	lwid <- c(lwid[1], 0.2, lwid[2])
-    }
-    lmat[is.na(lmat)] <- 0
+    if( missing(lhei) || is.null(lhei) )
+      lhei <- c(keysize, 4)
 
+    if( missing(lwid) || is.null(lwid) )
+       lwid <- c(keysize, 4)
+
+    if( missing(lmat) || is.null(lmat) )
+       {
+         lmat <- rbind(4:3, 2:1)
+         
+         if(!missing(ColSideColors)) { ## add middle row to layout
+           if(!is.character(ColSideColors) || length(ColSideColors) != nc)
+             stop("'ColSideColors' must be a character vector of length ncol(x)")
+           lmat <- rbind(lmat[1,]+1, c(NA,1), lmat[2,]+1)
+           lhei <- c(lhei[1], 0.2, lhei[2])
+         }
+
+         if(!missing(RowSideColors)) { ## add middle column to layout
+           if(!is.character(RowSideColors) || length(RowSideColors) != nr)
+             stop("'RowSideColors' must be a character vector of length nrow(x)")
+           lmat <- cbind(lmat[,1]+1, c(rep(NA, nrow(lmat)-1), 1), lmat[,2]+1)
+           lwid <- c(lwid[1], 0.2, lwid[2])
+         }
+
+         lmat[is.na(lmat)] <- 0
+       }
+       
+     if(length(lhei) != nrow(lmat))
+       stop("lhei must have length = nrow(lmat) = ", nrow(lmat))
+
+     if(length(lwid) != ncol(lmat))
+       stop("lwid must have length = ncol(lmat) =", ncol(lmat))
+
     ## Graphics `output' -----------------------
 
     op <- par(no.readonly = TRUE)

Modified: trunk/gplots/man/heatmap.2.Rd
===================================================================
--- trunk/gplots/man/heatmap.2.Rd	2008-03-27 22:36:13 UTC (rev 1251)
+++ trunk/gplots/man/heatmap.2.Rd	2008-04-07 16:47:30 UTC (rev 1252)
@@ -71,6 +71,11 @@
                      xlab = NULL,
                      ylab = NULL,
 
+                     # plot layout
+                     lmat = NULL,
+                     lhei = NULL,
+                     lwid = NULL,
+
                      # extras
                      ...
                      )
@@ -180,6 +185,9 @@
     0.25.}
   % plot labels
   \item{main, xlab, ylab}{main, x- and y-axis titles; defaults to none.}
+  % figure layout
+  \item{lmat, lhei, lwid}{visual layout: position matrix, column height,
+    column width.  See below for details}
   \item{...}{additional arguments passed on to \code{\link{image}} } %
 }
 \details{
@@ -209,7 +217,18 @@
   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
+  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},
+  \code{lwid}, and \code{lhei}.  \code{lmat} controls the relative
+  postition of each element, while \code{lwid} controls the column
+  width, and \code{lhei} controls the row height. See the help page for
+  \code{\link[graphics]{layout}} for details on how to use these
+  arguments.
 }
 \note{
   The original rows and columns are reordered \emph{in any case} to
@@ -276,7 +295,12 @@
  # without reorder
  heatmap.2(Ca, Rowv=FALSE, symm=TRUE, margin=c(6, 6), trace="none" )
 
+ ## Place the color key below the image plot
+ heatmap.2(x, lmat=rbind( c(0, 3), c(2,1), c(0,4) ), lhei=c(1.5, 4, 2 ) )
 
+ ## Place the color key to the top right of the image plot
+ heatmap.2(x, lmat=rbind( c(0, 3, 4), c(2,1,0 ) ), lwid=c(1.5, 4, 2 ) )
+
  ## For variable clustering, rather use distance based on cor():
  data(USJudgeRatings)
  symnum( cU <- cor(USJudgeRatings) )
@@ -312,5 +336,6 @@
                main="SpikeIn@pm Fold Changes\nrelative to 12.50 sample", 
                xlab="Relative Concentration", ylab="Probeset")
  }
+
 }
 \keyword{hplot}


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.