[R-gregmisc-users] SF.net SVN: r-gregmisc:[1780] trunk/gplots
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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1780] trunk/gplots
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From: <wa...@us...> - 2014-04-05 00:10:18
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Revision: 1780
http://sourceforge.net/p/r-gregmisc/code/1780
Author: warnes
Date: 2014-04-05 00:10:13 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Add 'extrafun' argument to heatmap.2 to allow the user to perform
additional customization by providing a function to be called before
heatmap.2 exits.
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 2014-04-04 22:37:12 UTC (rev 1779)
+++ trunk/gplots/R/heatmap.2.R 2014-04-05 00:10:13 UTC (rev 1780)
@@ -78,6 +78,7 @@
lwid = NULL,
## extras
+ extrafun=NULL,
...
)
{
@@ -641,9 +642,6 @@
}
}
-
-
-
}
else
plot.new()
@@ -655,6 +653,9 @@
color=retval$col
)
+ ## If user has provided an extra function, call it.
+ if(!is.null(extrafun))
+ extrafun()
invisible( retval )
}
Modified: trunk/gplots/man/heatmap.2.Rd
===================================================================
--- trunk/gplots/man/heatmap.2.Rd 2014-04-04 22:37:12 UTC (rev 1779)
+++ trunk/gplots/man/heatmap.2.Rd 2014-04-05 00:10:13 UTC (rev 1780)
@@ -3,7 +3,7 @@
\title{ Enhanced Heat Map }
\description{
A heat map is a false color image (basically
- \code{\link{image}(t(x))}) with a dendrogram added to the left side
+ \code{\link{image}(t(x))}) with a dendrogram added to the left side
and/or to the top. Typically, reordering of the rows and columns
according to some set of values (row or column means) within the
restrictions imposed by the dendrogram is carried out.
@@ -90,6 +90,7 @@
lwid = NULL,
# extras
+ extrafun=NULL,
...
)
}
@@ -112,7 +113,7 @@
\item{hclustfun}{function used to compute the hierarchical clustering
when \code{Rowv} or \code{Colv} are not dendrograms. Defaults to
\code{\link{hclust}}.}
- \item{dendrogram}{character string indicating whether to draw 'none',
+ \item{dendrogram}{character string indicating whether to draw 'none',
'row', 'column' or 'both' dendrograms. Defaults to 'both'. However,
if Rowv (or Colv) is FALSE or NULL and dendrogram is 'both', then a
warning is issued and Rowv (or Colv) arguments are honoured.}
@@ -182,12 +183,12 @@
for the row or column axis labeling. The defaults currently only
use number of rows or columns, respectively.}
\item{labRow, labCol}{character vectors with row and column labels to
- use; these default to \code{rownames(x)} or \code{colnames(x)},
+ 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).}
+ 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
@@ -211,7 +212,9 @@
% 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}} } %
+ \item{extrafun}{A function to be called after all other work. See
+ examples.}
+ \item{...}{additional arguments passed on to \code{\link{image}} }
}
\details{
If either \code{Rowv} or \code{Colv} are dendrograms they are honored
@@ -221,11 +224,11 @@
If either is a vector (of \dQuote{weights}) then the appropriate
dendrogram is reordered according to the supplied values subject to
- the constraints imposed by the dendrogram, by \code{\link{reorder}(dd,
+ the constraints imposed by the dendrogram, by \code{\link{reorder}(dd,
Rowv)}, in the row case.
%%
If either is missing, as by default, then the ordering of the
- corresponding dendrogram is by the mean value of the rows/columns,
+ corresponding dendrogram is by the mean value of the rows/columns,
i.e., in the case of rows, \code{Rowv <- rowMeans(x, na.rm=na.rm)}.
%%
If either is \code{\link{NULL}}, \emph{no reordering} will be done for
@@ -237,7 +240,7 @@
The default colors range from red to white (\code{heat.colors}) and
are not pretty. Consider using enhancements such
- as the \pkg{RColorBrewer} package,
+ as the \pkg{RColorBrewer} package,
\url{http://cran.r-project.org/src/contrib/PACKAGES.html#RColorBrewer}
to select better colors.
@@ -286,9 +289,9 @@
\item{hline}{center-line value used for row trace, present only if
\code{trace="both"} or \code{trace="row"} }
\item{colorTable}{A three-column data frame providing the lower and upper
- bound and color for each bin}
+ bound and color for each bin}
}
-\author{Andy Liaw, original; R. Gentleman, M. Maechler, W. Huber,
+\author{Andy Liaw, original; R. Gentleman, M. Maechler, W. Huber,
G. Warnes, revisions.}
\seealso{\code{\link{image}}, \code{\link{hclust}}}
@@ -303,7 +306,7 @@
##
## demonstrate the effect of row and column dendogram options
##
- heatmap.2(x) ## default - dendrogram plotted and reordering done.
+ heatmap.2(x) ## default - dendrogram plotted and reordering done.
heatmap.2(x, dendrogram="none") ## no dendrogram plotted, but reordering done.
heatmap.2(x, dendrogram="row") ## row dendrogram plotted and row reordering done.
heatmap.2(x, dendrogram="col") ## col dendrogram plotted and col reordering done.
@@ -341,7 +344,21 @@
heatmap.2(x, srtRow=0, srtCol=90, offsetRow=2, offsetCol=2)
heatmap.2(x, srtRow=0, srtCol=90, offsetRow=-1, offsetCol=-1)
- ##
+ ## Show how to use 'extrafun' to replace the 'key' with a scatterplot
+ lmat <- rbind( c(5,3,4), c(2,1,4) )
+ lhei <- c(1.5, 4)
+ lwid <- c(1.5, 4, 0.75)
+
+ myplot <- function() {
+ oldpar <- par("mar")
+ par(mar=c(5.1, 4.1, 0.5, 0.5))
+ plot(mpg ~ hp, data=x)
+ }
+
+ heatmap.2(x, lmat=lmat, lhei=lhei, lwid=lwid, key=FALSE, extrafun=myplot)
+
+
+ ##
## Show effect of z-score scaling within columns, blue-red color scale
##
hv <- heatmap.2(x, col=bluered, scale="column", tracecol="#303030")
@@ -364,18 +381,18 @@
##
## A more decorative heatmap, with z-score scaling along columns
##
- hv <- heatmap.2(x, col=cm.colors(255), scale="column",
- RowSideColors=rc, ColSideColors=cc, margin=c(5, 10),
- xlab="specification variables", ylab= "Car Models",
- main="heatmap(<Mtcars data>, ..., scale=\"column\")",
+ hv <- heatmap.2(x, col=cm.colors(255), scale="column",
+ RowSideColors=rc, ColSideColors=cc, margin=c(5, 10),
+ xlab="specification variables", ylab= "Car Models",
+ main="heatmap(<Mtcars data>, ..., scale=\"column\")",
tracecol="green", density="density")
## Note that the breakpoints are now symmetric about 0
-
+
%% want example using the `add.exp' argument!
data(attitude)
@@ -398,7 +415,7 @@
data(USJudgeRatings)
symnum( cU <- cor(USJudgeRatings) )
- hU <- heatmap.2(cU, Rowv=FALSE, symm=TRUE, col=topo.colors(16),
+ hU <- heatmap.2(cU, Rowv=FALSE, symm=TRUE, col=topo.colors(16),
distfun=function(c) as.dist(1 - c), trace="none")
## The Correlation matrix with same reordering:
@@ -407,8 +424,8 @@
# now with the correlation matrix on the plot itself
- heatmap.2(cU, Rowv=FALSE, symm=TRUE, col=rev(heat.colors(16)),
- distfun=function(c) as.dist(1 - c), trace="none",
+ heatmap.2(cU, Rowv=FALSE, symm=TRUE, col=rev(heat.colors(16)),
+ distfun=function(c) as.dist(1 - c), trace="none",
cellnote=hM)
## genechip data examples
@@ -418,15 +435,15 @@
pms <- SpikeIn@pm
# just the data, scaled across rows
- heatmap.2(pms, col=rev(heat.colors(16)), main="SpikeIn@pm",
- xlab="Relative Concentration", ylab="Probeset",
+ heatmap.2(pms, col=rev(heat.colors(16)), main="SpikeIn@pm",
+ xlab="Relative Concentration", ylab="Probeset",
scale="row")
# fold change vs "12.50" sample
data <- pms / pms[, "12.50"]
data <- ifelse(data>1, data, -1/data)
- heatmap.2(data, breaks=16, col=redgreen, tracecol="blue",
- main="SpikeIn@pm Fold Changes\nrelative to 12.50 sample",
+ heatmap.2(data, breaks=16, col=redgreen, tracecol="blue",
+ main="SpikeIn@pm Fold Changes\nrelative to 12.50 sample",
xlab="Relative Concentration", ylab="Probeset")
}
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