[R-gregmisc-users] SF.net SVN: r-gregmisc:[1724] trunk/gplots
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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1724] trunk/gplots
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From: <wa...@us...> - 2013-10-11 20:19:25
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Revision: 1724
http://sourceforge.net/p/r-gregmisc/code/1724
Author: warnes
Date: 2013-10-11 20:19:22 +0000 (Fri, 11 Oct 2013)
Log Message:
-----------
Add parameters to control row and column label positioning, rotation, justification, and offset.
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 2013-10-11 17:15:54 UTC (rev 1723)
+++ trunk/gplots/R/heatmap.2.R 2013-10-11 20:19:22 UTC (rev 1724)
@@ -52,6 +52,12 @@
cexCol = 0.2 + 1/log10(nc),
labRow = NULL,
labCol = NULL,
+ srtRow = NULL,
+ srtCol = NULL,
+ adjRow = c(0,NA),
+ adjCol = c(NA,0),
+ offsetRow = 0.5,
+ offsetCol = 0.5,
## color key + density info
key = TRUE,
@@ -389,10 +395,79 @@
col=na.color, add=TRUE)
}
- ## add labels
- axis(1, 1:nc, labels= labCol, las= 2, line= -0.5, tick= 0, cex.axis= cexCol)
+ ## add column labels
+ if(is.null(srtCol))
+ axis(1,
+ 1:nc,
+ labels= labCol,
+ las= 2,
+ line= -0.5 + offsetCol,
+ tick= 0,
+ cex.axis= cexCol,
+ hadj=adjCol[1],
+ padj=adjCol[2]
+ )
+ else
+ {
+ if(is.numeric(srtCol))
+ {
+ if(missing(adjCol) || is.null(adjCol))
+ adjCol=c(1,NA)
+
+ xpd.orig <- par("xpd")
+ par(xpd=NA)
+ xpos <- axis(1, 1:nc, labels=rep("", nc), las=2, tick=0)
+ text(x=xpos,
+ y=par("usr")[3] - (1.0 + offsetCol) * strheight("M"),
+ labels=labCol,
+ ##pos=1,
+ adj=adjCol,
+ cex=cexCol,
+ srt=srtCol)
+ par(xpd=xpd.orig)
+ }
+ else
+ warning("Invalid value for srtCol ignored.")
+ }
+
+ ## add row labels
+ if(is.null(srtRow))
+ {
+ axis(4,
+ iy,
+ labels=labRow,
+ las=2,
+ line=-0.5+offsetRow,
+ tick=0,
+ cex.axis=cexRow,
+ hadj=adjRow[1],
+ padj=adjRow[2]
+ )
+ }
+ else
+ {
+ if(is.numeric(srtRow))
+ {
+ xpd.orig <- par("xpd")
+ par(xpd=NA)
+ ypos <- axis(4, iy, labels=rep("", nr), las=2, line= -0.5, tick=0)
+ text(x=par("usr")[2] + (1.0 + offsetRow) * strwidth("M"),
+ y=ypos,
+ labels=labRow,
+ adj=adjRow,
+ cex=cexRow,
+ srt=srtRow
+ )
+ par(xpd=xpd.orig)
+ }
+ else
+ warning("Invalid value for srtRow ignored.")
+ }
+
+
+
+ ## add row and column headings (xlab, ylab)
if(!is.null(xlab)) mtext(xlab, side = 1, line = margins[1] - 1.25)
- axis(4, iy, labels= labRow, las= 2, line= -0.5, tick= 0, cex.axis= cexRow)
if(!is.null(ylab)) mtext(ylab, side = 4, line = margins[2] - 1.25)
## perform user-specified function
Modified: trunk/gplots/man/heatmap.2.Rd
===================================================================
--- trunk/gplots/man/heatmap.2.Rd 2013-10-11 17:15:54 UTC (rev 1723)
+++ trunk/gplots/man/heatmap.2.Rd 2013-10-11 20:19:22 UTC (rev 1724)
@@ -64,6 +64,12 @@
cexCol = 0.2 + 1/log10(nc),
labRow = NULL,
labCol = NULL,
+ srtRow = NULL,
+ srtCol = NULL,
+ adjRow = c(0,NA),
+ adjCol = c(NA,0),
+ offsetRow = 0.5,
+ offsetCol = 0.5,
# color key + density info
key = TRUE,
@@ -178,6 +184,12 @@
\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{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.}
% 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}
@@ -302,6 +314,33 @@
heatmap.2(x, Rowv=NULL, dendrogram="both") ## generate warning!
heatmap.2(x, Colv=FALSE, dendrogram="both") ## generate warning!
+ ## Show effect of row and column label rotation
+ heatmap.2(x, srtCol=NULL)
+ heatmap.2(x, srtCol=0, adjCol = c(0.5,1) )
+ heatmap.2(x, srtCol=45, adjCol = c(1,1) )
+ heatmap.2(x, srtCol=135, adjCol = c(1,0) )
+ heatmap.2(x, srtCol=180, adjCol = c(0.5,0) )
+ heatmap.2(x, srtCol=225, adjCol = c(0,0) ) ## not very useful
+ heatmap.2(x, srtCol=270, adjCol = c(0,0.5) )
+ heatmap.2(x, srtCol=315, adjCol = c(0,1) )
+ heatmap.2(x, srtCol=360, adjCol = c(0.5,1) )
+
+ heatmap.2(x, srtRow=45, adjRow=c(0, 1) )
+ heatmap.2(x, srtRow=45, adjRow=c(0, 1), srtCol=45, adjCol=c(1,1) )
+ heatmap.2(x, srtRow=45, adjRow=c(0, 1), srtCol=270, adjCol=c(0,0.5) )
+
+ ## Show effect of offsetRow/offsetCol (only works when srtRow/srtCol is
+ ## not also present)
+ heatmap.2(x, offsetRow=0, offsetCol=0)
+ heatmap.2(x, offsetRow=1, offsetCol=1)
+ heatmap.2(x, offsetRow=2, offsetCol=2)
+ heatmap.2(x, offsetRow=-1, offsetCol=-1)
+
+ heatmap.2(x, srtRow=0, srtCol=90, offsetRow=0, offsetCol=0)
+ heatmap.2(x, srtRow=0, srtCol=90, offsetRow=1, offsetCol=1)
+ heatmap.2(x, srtRow=0, srtCol=90, offsetRow=2, offsetCol=2)
+ heatmap.2(x, srtRow=0, srtCol=90, offsetRow=-1, offsetCol=-1)
+
##
## Show effect of z-score scaling within columns, blue-red color scale
##
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