[R-gregmisc-users] SF.net SVN: r-gregmisc:[1930] trunk/gplots
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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1930] trunk/gplots
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From: <wa...@us...> - 2015-04-22 21:33:14
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Revision: 1930
http://sourceforge.net/p/r-gregmisc/code/1930
Author: warnes
Date: 2015-04-22 21:33:06 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
heatmap.2: add new 'colRow' and 'colCol' arguments to control the color of row and column text labels
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 2015-04-14 22:02:42 UTC (rev 1929)
+++ trunk/gplots/R/heatmap.2.R 2015-04-22 21:33:06 UTC (rev 1930)
@@ -59,6 +59,8 @@
adjCol = c(NA,0),
offsetRow = 0.5,
offsetCol = 0.5,
+ colRow = NULL,
+ colCol = NULL,
## color key + density info
key = TRUE,
@@ -281,6 +283,12 @@
labCol <- if(is.null(colnames(x))) (1:nc)[colInd] else colnames(x)
else
labCol <- labCol[colInd]
+
+ if(!is.null(colRow))
+ colRow <- colRow[rowInd]
+
+ if(!is.null(colCol))
+ colCol <- colCol[colInd]
if(scale == "row") {
retval$rowMeans <- rm <- rowMeans(x, na.rm = na.rm)
@@ -415,7 +423,7 @@
}
## add column labels
- if(is.null(srtCol))
+ if(is.null(srtCol) && is.null(colCol))
axis(1,
1:nc,
labels= labCol,
@@ -428,7 +436,7 @@
)
else
{
- if(is.numeric(srtCol))
+ if(is.null(srtCol) || is.numeric(srtCol))
{
if(missing(adjCol) || is.null(adjCol))
adjCol=c(1,NA)
@@ -442,7 +450,10 @@
##pos=1,
adj=adjCol,
cex=cexCol,
- srt=srtCol)
+ srt=srtCol,
+ col=colCol
+ )
+ print(colCol)
par(xpd=xpd.orig)
}
else
@@ -450,7 +461,7 @@
}
## add row labels
- if(is.null(srtRow))
+ if(is.null(srtRow) && is.null(colRow))
{
axis(4,
iy,
@@ -465,7 +476,7 @@
}
else
{
- if(is.numeric(srtRow))
+ if(is.null(srtRow) || is.numeric(srtRow))
{
xpd.orig <- par("xpd")
par(xpd=NA)
@@ -475,7 +486,8 @@
labels=labRow,
adj=adjRow,
cex=cexRow,
- srt=srtRow
+ srt=srtRow,
+ col=colRow
)
par(xpd=xpd.orig)
}
Modified: trunk/gplots/man/heatmap.2.Rd
===================================================================
--- trunk/gplots/man/heatmap.2.Rd 2015-04-14 22:02:42 UTC (rev 1929)
+++ trunk/gplots/man/heatmap.2.Rd 2015-04-22 21:33:06 UTC (rev 1930)
@@ -71,6 +71,8 @@
adjCol = c(NA,0),
offsetRow = 0.5,
offsetCol = 0.5,
+ colRow = NULL,
+ colCol = NULL,
# color key + density info
key = TRUE,
@@ -111,10 +113,11 @@
\code{\link{dendrogram}}, then it is used "as-is", ie
without any reordering. If a vector of integers, then dendrogram is
computed and reordered based on the order of the vector.}
- \item{Colv}{determines if and how the \emph{column} dendrogram should be
- reordered. Has the options as the \code{Rowv} argument above and
- \emph{additionally} when \code{x} is a square matrix, \code{Colv =
- "Rowv"} means that columns should be treated identically to the rows.}
+ \item{Colv}{determines if and how the \emph{column} dendrogram should
+ be reordered. Has the options as the \code{Rowv} argument above and
+ \emph{additionally} when \code{x} is a square matrix,
+ \code{Colv="Rowv"} means that columns should be treated identically
+ to the rows.}
\item{distfun}{function used to compute the distance (dissimilarity)
between both rows and columns. Defaults to \code{\link{dist}}.}
\item{hclustfun}{function used to compute the hierarchical clustering
@@ -128,7 +131,8 @@
reordering the row and column dendrograms. The default uses
\code{\link{stats}{reorder.dendrogram}} }.
\item{symm}{logical indicating if \code{x} should be treated
- \bold{symm}etrically; can only be true when \code{x} is a square matrix.}
+ \bold{symm}etrically; can only be true when \code{x} is a
+ square matrix.}
% data scaling
\item{scale}{character indicating if the values should be centered and
scaled in either the row direction or the column direction, or
@@ -150,12 +154,14 @@
\item{col}{colors used for the image. Defaults to heat colors
(\code{heat.colors}).}
% block separation
- \item{colsep, rowsep, sepcolor}{(optional) vector of integers indicating
- which columns or rows should be separated from the preceding columns
- or rows by a narrow space of color \code{sepcolor}.}
- \item{sepwidth}{(optional) Vector of length 2 giving the width (colsep) or height (rowsep) the separator box
- drawn by colsep and rowsep as a function of the width (colsep) or
- height (rowsep) of a cell. Defaults to \code{c(0.05, 0.05)}}
+ \item{colsep, rowsep, sepcolor}{(optional) vector of integers
+ indicating which columns or rows should be separated from the
+ preceding columns or rows by a narrow space of color
+ \code{sepcolor}.}
+ \item{sepwidth}{(optional) Vector of length 2 giving the width
+ (colsep) or height (rowsep) the separator box drawn by colsep and
+ rowsep as a function of the width (colsep) or height (rowsep) of a
+ cell. Defaults to \code{c(0.05, 0.05)}}
% cell labeling
\item{cellnote}{(optional) matrix of character strings which will be
placed within each color cell, e.g. p-value symbols.}
@@ -181,25 +187,31 @@
defaults to the value of \code{tracecol}.}
% Row/Column Labeling
\item{margins}{numeric vector of length 2 containing the margins
- (see \code{\link{par}(mar= *)}) for column and row names, respectively.}
- \item{ColSideColors}{(optional) character vector of length \code{ncol(x)}
- containing the color names for a horizontal side bar that may be used to
- annotate the columns of \code{x}.}
- \item{RowSideColors}{(optional) character vector of length \code{nrow(x)}
- containing the color names for a vertical side bar that may be used to
- annotate the rows of \code{x}.}
+ (see \code{\link{par}(mar= *)}) for column and row names,
+ respectively.}
+ \item{ColSideColors}{(optional) character vector of length
+ \code{ncol(x)} containing the color names for a horizontal side bar
+ that may be used to annotate the columns of \code{x}.}
+ \item{RowSideColors}{(optional) character vector of length
+ \code{nrow(x)} containing the color names for a vertical side bar
+ that may be used to annotate the rows of \code{x}.}
\item{cexRow, cexCol}{positive numbers, used as \code{cex.axis} in
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)},
respectively.}
- \item{srtRow, srtCol}{angle of row/column labels, in degrees from horizontal}
+ \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.}
+ orientation).}
+ \item{offsetRow, offsetCol}{Number of character-width spaces to
+ place between row/column labels and the edge of the plotting
+ region.}
+ \item{colRow, colCol}{color of row/column labels, either a scalar to
+ set the color of all labels the same, or a vector providing the
+ colors of each label item}
% 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}
@@ -226,8 +238,8 @@
the xaxis of the color key. Returns a named list containing
parameters that can be passed to \code{axis}. See examples.}
\item{key.ytickfun}{function computing tick location and labels for
- the y axis of the color key. Returns a named list containing
- parameters that can be passed to \code{axis}. See examples.}
+ the y axis of the color key. Returns a named list containing
+ parameters that can be passed to \code{axis}. See examples.}
\item{key.par}{graphical parameters for the color key. Named list that
can be passed to \code{par}.}
% plot labels
@@ -446,14 +458,19 @@
RowSideColors=rc, ColSideColors=cc, margin=c(5, 10),
xlab="specification variables", ylab= "Car Models",
main="heatmap(<Mtcars data>, ..., scale=\"column\")",
- tracecol="green", density="density")
+ tracecol="green", density="density")
## Note that the breakpoints are now symmetric about 0
+
+ ## Color the labels to match RowSideColors and ColSideColors
+ 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", colRow=rc, colCol=cc,
+ srtCol=45, adjCol=c(0.5,1))
+
-
-
-
-
%% want example using the `add.exp' argument!
data(attitude)
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