[R-gregmisc-users] SF.net SVN: r-gregmisc:[1317] trunk/gplots
Brought to you by:
warnes
Menu
▾
▴
[R-gregmisc-users] SF.net SVN: r-gregmisc:[1317] trunk/gplots
|
From: <wa...@us...> - 2009-05-08 21:55:20
|
Revision: 1317
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1317&view=rev
Author: warnes
Date: 2009-05-08 21:55:05 +0000 (Fri, 08 May 2009)
Log Message:
-----------
heatmap.2: Add option to create breakpoints symmetric around 0, provide additional information in the return value
Modified Paths:
--------------
trunk/gplots/R/heatmap.2.R
trunk/gplots/man/heatmap.2.Rd
trunk/gplots/tests/heatmap2Test.Rout.save
Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R 2009-05-08 21:27:55 UTC (rev 1316)
+++ trunk/gplots/R/heatmap.2.R 2009-05-08 21:55:05 UTC (rev 1317)
@@ -1,164 +1,177 @@
-# $Id$
+## $Id$
heatmap.2 <- function (x,
- # dendrogram control
- Rowv = TRUE,
- Colv=if(symm)"Rowv" else TRUE,
- distfun = dist,
- hclustfun = hclust,
- dendrogram = c("both","row","column","none"),
- symm = FALSE,
+ ## dendrogram control
+ Rowv = TRUE,
+ Colv=if(symm)"Rowv" else TRUE,
+ distfun = dist,
+ hclustfun = hclust,
+ dendrogram = c("both","row","column","none"),
+ symm = FALSE,
- # data scaling
- scale = c("none","row", "column"),
- na.rm=TRUE,
+ ## data scaling
+ scale = c("none","row", "column"),
+ na.rm=TRUE,
- # image plot
- revC = identical(Colv, "Rowv"),
- add.expr,
- breaks,
- col="heat.colors",
+ ## image plot
+ revC = identical(Colv, "Rowv"),
+ add.expr,
- # block sepration
- colsep,
- rowsep,
- sepcolor="white",
- sepwidth=c(0.05,0.05),
+ ## mapping data to colors
+ breaks,
+ symbreaks=min(x < 0, na.rm=TRUE) || scale!="none",
- # cell labeling
- cellnote,
- notecex=1.0,
- notecol="cyan",
- na.color=par("bg"),
+ ## colors
+ col="heat.colors",
- # level trace
- trace=c("column","row","both","none"),
- tracecol="cyan",
- hline=median(breaks),
- vline=median(breaks),
- linecol=tracecol,
+ ## block sepration
+ colsep,
+ rowsep,
+ sepcolor="white",
+ sepwidth=c(0.05,0.05),
- # Row/Column Labeling
- margins = c(5, 5),
- ColSideColors,
- RowSideColors,
- cexRow = 0.2 + 1/log10(nr),
- cexCol = 0.2 + 1/log10(nc),
- labRow = NULL,
- labCol = NULL,
+ ## cell labeling
+ cellnote,
+ notecex=1.0,
+ notecol="cyan",
+ na.color=par("bg"),
- # color key + density info
- key = TRUE,
- keysize = 1.5,
- density.info=c("histogram","density","none"),
- denscol=tracecol,
- #symkey = TRUE, # should be something like
- symkey = min(x < 0, na.rm=TRUE),
- densadj = 0.25,
+ ## level trace
+ trace=c("column","row","both","none"),
+ tracecol="cyan",
+ hline=median(breaks),
+ vline=median(breaks),
+ linecol=tracecol,
- # plot labels
- main = NULL,
- xlab = NULL,
- ylab = NULL,
+ ## Row/Column Labeling
+ margins = c(5, 5),
+ ColSideColors,
+ RowSideColors,
+ cexRow = 0.2 + 1/log10(nr),
+ cexCol = 0.2 + 1/log10(nc),
+ labRow = NULL,
+ labCol = NULL,
- # plot layout
- lmat = NULL,
- lhei = NULL,
- lwid = NULL,
+ ## color key + density info
+ key = TRUE,
+ keysize = 1.5,
+ density.info=c("histogram","density","none"),
+ denscol=tracecol,
+ symkey = min(x < 0, na.rm=TRUE) || symbreaks,
+ densadj = 0.25,
- # extras
- ...
- )
+ ## plot labels
+ main = NULL,
+ xlab = NULL,
+ ylab = NULL,
+
+ ## plot layout
+ lmat = NULL,
+ lhei = NULL,
+ lwid = NULL,
+
+ ## extras
+ ...
+ )
{
scale01 <- function(x, low=min(x), high=max(x) )
{
x <- (x-low)/(high - low)
x
}
+
+ retval <- list()
+
+ scale <- if(symm && missing(scale)) "none" else match.arg(scale)
+ dendrogram <- match.arg(dendrogram)
+ trace <- match.arg(trace)
+ density.info <- match.arg(density.info)
- scale <- if(symm && missing(scale)) "none" else match.arg(scale)
- dendrogram <- match.arg(dendrogram)
- trace <- match.arg(trace)
- density.info <- match.arg(density.info)
+ if(length(col)==1 && is.character(col) )
+ col <- get(col, mode="function")
- if(!missing(breaks) && (scale!="none"))
- warning("Using scale=\"row\" or scale=\"column\" when breaks are",
- "specified can produce unpredictable results.",
- "Please consider using only one or the other.")
+ if(!missing(breaks) && (scale!="none"))
+ warning("Using scale=\"row\" or scale=\"column\" when breaks are",
+ "specified can produce unpredictable results.",
+ "Please consider using only one or the other.")
- # key & density don't make sense when data is not all on the same scale
-# if(scale!="none" && key==TRUE)
-# {
-# warning("Key cannot be plotted when scale!=\"none\".")
-# key=FALSE
-# }
+ ## key & density don't make sense when data is not all on the same scale
+ ## if(scale!="none" && key==TRUE)
+ ## {
+ ## warning("Key cannot be plotted when scale!=\"none\".")
+ ## key=FALSE
+ ## }
-
-
- if ( (Colv=="Rowv") && (!isTRUE(Rowv) || is.null(Rowv) ) )
+ if ( is.null(Rowv) )
+ Rowv <- FALSE
+ if ( is.null(Colv) )
Colv <- FALSE
+ else if( Colv=="Rowv" && !isTRUE(Rowv) )
+ Colv <- FALSE
- if(length(di <- dim(x)) != 2 || !is.numeric(x))
- stop("`x' must be a numeric matrix")
+
+ if(length(di <- dim(x)) != 2 || !is.numeric(x))
+ stop("`x' must be a numeric matrix")
- nr <- di[1]
- nc <- di[2]
+ nr <- di[1]
+ nc <- di[2]
- if(nr <= 1 || nc <= 1)
- stop("`x' must have at least 2 rows and 2 columns")
+ if(nr <= 1 || nc <= 1)
+ stop("`x' must have at least 2 rows and 2 columns")
- if(!is.numeric(margins) || length(margins) != 2)
- stop("`margins' must be a numeric vector of length 2")
+ if(!is.numeric(margins) || length(margins) != 2)
+ stop("`margins' must be a numeric vector of length 2")
- if(missing(cellnote))
- cellnote <- matrix("", ncol=ncol(x), nrow=nrow(x))
+ if(missing(cellnote))
+ cellnote <- matrix("", ncol=ncol(x), nrow=nrow(x))
- if(!inherits(Rowv, "dendrogram")) {
- ## Check if Rowv and dendrogram arguments are consistent
- if ( ( (!isTRUE(Rowv)) || (is.null(Rowv))) && (dendrogram %in% c("both","row") ) )
- {
- if (is.logical(Colv) && (Colv))
- dendrogram <- "column"
- else
- dedrogram <- "none"
-
- warning("Discrepancy: Rowv is FALSE, while dendrogram is `",
- dendrogram, "'. Omitting row dendogram.")
-
+ if(!inherits(Rowv, "dendrogram")) {
+ ## Check if Rowv and dendrogram arguments are consistent
+ if ( ( (!isTRUE(Rowv)) || (is.null(Rowv))) &&
+ (dendrogram %in% c("both","row") ) )
+ {
+ if (is.logical(Colv) && (Colv))
+ dendrogram <- "column"
+ else
+ dedrogram <- "none"
+
+ warning("Discrepancy: Rowv is FALSE, while dendrogram is `",
+ dendrogram, "'. Omitting row dendogram.")
+
+ }
}
-}
- if(!inherits(Colv, "dendrogram")) {
- ## Check if Colv and dendrogram arguments are consistent
- if ( ( (!isTRUE(Colv)) || (is.null(Colv)))
- && (dendrogram %in% c("both","column")) )
- {
- if (is.logical(Rowv) && (Rowv))
- dendrogram <- "row"
- else
- dendrogram <- "none"
-
- warning("Discrepancy: Colv is FALSE, while dendrogram is `",
- dendrogram, "'. Omitting column dendogram.")
- }
-}
+ if(!inherits(Colv, "dendrogram")) {
+ ## Check if Colv and dendrogram arguments are consistent
+ if ( ( (!isTRUE(Colv)) || (is.null(Colv)))
+ && (dendrogram %in% c("both","column")) )
+ {
+ if (is.logical(Rowv) && (Rowv))
+ dendrogram <- "row"
+ else
+ dendrogram <- "none"
+
+ warning("Discrepancy: Colv is FALSE, while dendrogram is `",
+ dendrogram, "'. Omitting column dendogram.")
+ }
+ }
## by default order by row/col mean
## if(is.null(Rowv)) Rowv <- rowMeans(x, na.rm = na.rm)
## if(is.null(Colv)) Colv <- colMeans(x, na.rm = na.rm)
- ## get the dendrograms and reordering indices
+ ## get the dendrograms and reordering indices
- ## if( dendrogram %in% c("both","row") )
- ## { ## dendrogram option is used *only* for display purposes
+ ## if( dendrogram %in% c("both","row") )
+ ## { ## dendrogram option is used *only* for display purposes
if(inherits(Rowv, "dendrogram"))
{
ddr <- Rowv ## use Rowv 'as-is', when it is dendrogram
rowInd <- order.dendrogram(ddr)
}
-else if (is.integer(Rowv))
+ else if (is.integer(Rowv))
{ ## Compute dendrogram and do reordering based on given vector
hcr <- hclustfun(distfun(x))
ddr <- as.dendrogram(hcr)
@@ -208,308 +221,342 @@
if(nc != length(colInd))
stop("column dendrogram ordering gave index of wrong length")
}
-else if (isTRUE(Colv))
- {## If TRUE, compute dendrogram and do reordering based on rowMeans
- Colv <- colMeans(x, na.rm = na.rm)
- hcc <- hclustfun(distfun(if(symm)x else t(x)))
- ddc <- as.dendrogram(hcc)
- ddc <- reorder(ddc, Colv)
+ else if (isTRUE(Colv))
+ {## If TRUE, compute dendrogram and do reordering based on rowMeans
+ Colv <- colMeans(x, na.rm = na.rm)
+ hcc <- hclustfun(distfun(if(symm)x else t(x)))
+ ddc <- as.dendrogram(hcc)
+ ddc <- reorder(ddc, Colv)
- colInd <- order.dendrogram(ddc)
- if(nc != length(colInd))
- stop("column dendrogram ordering gave index of wrong length")
- }
-else
- {
- colInd <- 1:nc
- }
+ colInd <- order.dendrogram(ddc)
+ if(nc != length(colInd))
+ stop("column dendrogram ordering gave index of wrong length")
+ }
+ else
+ {
+ colInd <- 1:nc
+ }
+
+ retval$rowInd <- rowInd
+ retval$colInd <- colInd
+ retval$call <- match.call()
+
- ## reorder x & cellnote
- x <- x[rowInd, colInd]
- x.unscaled <- x
- cellnote <- cellnote[rowInd, colInd]
+ ## reorder x & cellnote
+ x <- x[rowInd, colInd]
+ x.unscaled <- x
+ cellnote <- cellnote[rowInd, colInd]
- if(is.null(labRow))
- labRow <- if(is.null(rownames(x))) (1:nr)[rowInd] else rownames(x)
- else
- labRow <- labRow[rowInd]
+ if(is.null(labRow))
+ labRow <- if(is.null(rownames(x))) (1:nr)[rowInd] else rownames(x)
+ else
+ labRow <- labRow[rowInd]
- if(is.null(labCol))
- labCol <- if(is.null(colnames(x))) (1:nc)[colInd] else colnames(x)
- else
- labCol <- labCol[colInd]
+ if(is.null(labCol))
+ labCol <- if(is.null(colnames(x))) (1:nc)[colInd] else colnames(x)
+ else
+ labCol <- labCol[colInd]
- if(scale == "row") {
- x <- sweep(x, 1, rowMeans(x, na.rm = na.rm))
- sx <- apply(x, 1, sd, na.rm = na.rm)
- x <- sweep(x, 1, sx, "/")
- }
- else if(scale == "column") {
- x <- sweep(x, 2, colMeans(x, na.rm = na.rm))
- sx <- apply(x, 2, sd, na.rm = na.rm)
- x <- sweep(x, 2, sx, "/")
- }
+ if(scale == "row") {
+ retval$rowMeans <- rm <- rowMeans(x, na.rm = na.rm)
+ x <- sweep(x, 1, rm)
+ retval$rowSDs <- sx <- apply(x, 1, sd, na.rm = na.rm)
+ x <- sweep(x, 1, sx, "/")
+ }
+ else if(scale == "column") {
+ retval$colMeans <- rm <- colMeans(x, na.rm = na.rm)
+ x <- sweep(x, 2, rm)
+ retval$colSDs <- sx <- apply(x, 2, sd, na.rm = na.rm)
+ x <- sweep(x, 2, sx, "/")
+ }
- ## Set up breaks and force values outside the range into the endmost bins
- if(missing(breaks) || is.null(breaks) || length(breaks)<1 )
- if(missing(col))
+ ## Set up breaks and force values outside the range into the endmost bins
+ if(missing(breaks) || is.null(breaks) || length(breaks)<1 )
+ {
+ if( missing(col) || is.function(col) )
breaks <- 16
- else
+ else
breaks <- length(col)+1
- if(length(breaks)==1)
- {
+ }
+
+ if(length(breaks)==1)
+ {
+ if(!symbreaks)
breaks <- seq( min(x, na.rm=na.rm), max(x,na.rm=na.rm), length=breaks)
- }
+ else
+ {
+ extreme <- max(abs(x), na.rm=TRUE)
+ breaks <- seq( -extreme, extreme, length=breaks )
+ }
+ }
- nbr <- length(breaks)
- ncol <- length(breaks)-1
+ nbr <- length(breaks)
+ ncol <- length(breaks)-1
- if(class(col)=="function")
- col <- col(ncol)
- else if(is.character(col) && length(col)==1)
- col <- do.call(col,list(ncol))
+ if(class(col)=="function")
+ col <- col(ncol)
- min.breaks <- min(breaks)
- max.breaks <- max(breaks)
+ min.breaks <- min(breaks)
+ max.breaks <- max(breaks)
- x[] <- ifelse(x<min.breaks, min.breaks, x)
- x[] <- ifelse(x>max.breaks, max.breaks, x)
+ x[x<min.breaks] <- min.breaks
+ x[x>max.breaks] <- max.breaks
-
-
+ ## Calculate the plot layout
+ if( missing(lhei) || is.null(lhei) )
+ lhei <- c(keysize, 4)
-
- ## Calculate the plot layout
- if( missing(lhei) || is.null(lhei) )
- lhei <- c(keysize, 4)
+ if( missing(lwid) || is.null(lwid) )
+ lwid <- 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(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])
+ }
- 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))
- 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))
- if(length(lwid) != ncol(lmat))
- stop("lwid must have length = ncol(lmat) =", ncol(lmat))
+ ## Graphics `output' -----------------------
- ## Graphics `output' -----------------------
+ op <- par(no.readonly = TRUE)
+ on.exit(par(op))
+ layout(lmat, widths = lwid, heights = lhei, respect = FALSE)
- op <- par(no.readonly = TRUE)
- on.exit(par(op))
- layout(lmat, widths = lwid, heights = lhei, respect = FALSE)
-
- ## draw the side bars
- if(!missing(RowSideColors)) {
- par(mar = c(margins[1],0, 0,0.5))
- image(rbind(1:nr), col = RowSideColors[rowInd], axes = FALSE)
+ ## draw the side bars
+ if(!missing(RowSideColors)) {
+ par(mar = c(margins[1],0, 0,0.5))
+ image(rbind(1:nr), col = RowSideColors[rowInd], axes = FALSE)
+ }
+ if(!missing(ColSideColors)) {
+ par(mar = c(0.5,0, 0,margins[2]))
+ image(cbind(1:nc), col = ColSideColors[colInd], axes = FALSE)
+ }
+ ## draw the main carpet
+ par(mar = c(margins[1], 0, 0, margins[2]))
+ if(!symm || scale != "none")
+ {
+ x <- t(x)
+ cellnote <- t(cellnote)
}
- if(!missing(ColSideColors)) {
- par(mar = c(0.5,0, 0,margins[2]))
- image(cbind(1:nc), col = ColSideColors[colInd], axes = FALSE)
+ if(revC)
+ { ## x columns reversed
+ iy <- nr:1
+ if(exists("ddr"))
+ ddr <- rev(ddr)
+ x <- x[,iy]
+ cellnote <- cellnote[,iy]
}
- ## draw the main carpet
- par(mar = c(margins[1], 0, 0, margins[2]))
- if(!symm || scale != "none")
- {
- x <- t(x)
- cellnote <- t(cellnote)
- }
- if(revC)
- { # x columns reversed
- iy <- nr:1
- ddr <- rev(ddr)
- x <- x[,iy]
- cellnote <- cellnote[,iy]
- }
- else iy <- 1:nr
+ else iy <- 1:nr
- image(1:nc, 1:nr, x, xlim = 0.5+ c(0, nc), ylim = 0.5+ c(0, nr),
- axes = FALSE, xlab = "", ylab = "", col=col, breaks=breaks,
- ...)
+ ## display the main carpet
+ image(1:nc, 1:nr, x, xlim = 0.5+ c(0, nc), ylim = 0.5+ c(0, nr),
+ axes = FALSE, xlab = "", ylab = "", col=col, breaks=breaks,
+ ...)
+ retval$carpet <- x
+ if(exists("ddr"))
+ retval$rowDendrogram <- ddr
+ if(exists("ddc"))
+ retval$colDendrogram <- ddc
+ retval$breaks <- breaks
+ retval$col <- col
+
+ ## fill 'na' positions with na.color
+ if(!invalid(na.color) & any(is.na(x)))
+ {
+ mmat <- ifelse(is.na(x), 1, NA)
+ image(1:nc, 1:nr, mmat, axes = FALSE, xlab = "", ylab = "",
+ col=na.color, add=TRUE)
+ }
- if(!invalid(na.color) & any(is.na(x)))
- {
- mmat <- ifelse(is.na(x), 1, NA)
- image(1:nc, 1:nr, mmat, axes = FALSE, xlab = "", ylab = "",
- col=na.color, add=TRUE)
- }
+ ## add labels
+ axis(1, 1:nc, labels= labCol, las= 2, line= -0.5, tick= 0, cex.axis= cexCol)
+ 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
+ if (!missing(add.expr))
+ eval(substitute(add.expr))
- axis(1, 1:nc, labels= labCol, las= 2, line= -0.5, tick= 0, cex.axis= cexCol)
- 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)
+ ## add 'background' colored spaces to visually separate sections
+ if(!missing(colsep))
+ for(csep in colsep)
+ rect(xleft =csep+0.5, ybottom=rep(0,length(csep)),
+ xright=csep+0.5+sepwidth[1], ytop=rep(ncol(x)+1,csep),
+ lty=1, lwd=1, col=sepcolor, border=sepcolor)
- if (!missing(add.expr))
- eval(substitute(add.expr))
+ if(!missing(rowsep))
+ for(rsep in rowsep)
+ rect(xleft =0, ybottom= (ncol(x)+1-rsep)-0.5,
+ xright=nrow(x)+1, ytop = (ncol(x)+1-rsep)-0.5 - sepwidth[2],
+ lty=1, lwd=1, col=sepcolor, border=sepcolor)
- ## add 'background' colored spaces to visually separate sections
- if(!missing(colsep))
- for(csep in colsep)
- rect(xleft =csep+0.5, ybottom=rep(0,length(csep)),
- xright=csep+0.5+sepwidth[1], ytop=rep(ncol(x)+1,csep),
- lty=1, lwd=1, col=sepcolor, border=sepcolor)
+
+ ## show traces
+ min.scale <- min(breaks)
+ max.scale <- max(breaks)
+ x.scaled <- scale01(t(x), min.scale, max.scale)
- if(!missing(rowsep))
- for(rsep in rowsep)
- rect(xleft =0, ybottom= (ncol(x)+1-rsep)-0.5,
- xright=nrow(x)+1, ytop = (ncol(x)+1-rsep)-0.5 - sepwidth[2],
- lty=1, lwd=1, col=sepcolor, border=sepcolor)
+ if(trace %in% c("both","column") )
+ {
+ retval$vline <- vline
+ vline.vals <- scale01(vline, min.scale, max.scale)
+ for( i in colInd )
+ {
+ if(!is.null(vline))
+ {
+ abline(v=i-0.5 + vline.vals, col=linecol, lty=2)
+ }
+ xv <- rep(i, nrow(x.scaled)) + x.scaled[,i] - 0.5
+ xv <- c(xv[1], xv)
+ yv <- 1:length(xv)-0.5
+ lines(x=xv, y=yv, lwd=1, col=tracecol, type="s")
+ }
+ }
- # show traces
- min.scale <- min(breaks)
- max.scale <- max(breaks)
- x.scaled <- scale01(t(x), min.scale, max.scale)
+ if(trace %in% c("both","row") )
+ {
+ retval$hline <- hline
+ hline.vals <- scale01(hline, min.scale, max.scale)
+ for( i in rowInd )
+ {
+ if(!is.null(hline))
+ {
+ abline(h=i + hline, col=linecol, lty=2)
+ }
+ yv <- rep(i, ncol(x.scaled)) + x.scaled[i,] - 0.5
+ yv <- rev(c(yv[1], yv))
+ xv <- length(yv):1-0.5
+ lines(x=xv, y=yv, lwd=1, col=tracecol, type="s")
+ }
+ }
- if(trace %in% c("both","column") )
- {
- for( i in colInd )
- {
- if(!is.null(vline))
- {
- vline.vals <- scale01(vline, min.scale, max.scale)
- abline(v=i-0.5 + vline.vals, col=linecol, lty=2)
- }
- xv <- rep(i, nrow(x.scaled)) + x.scaled[,i] - 0.5
- xv <- c(xv[1], xv)
- yv <- 1:length(xv)-0.5
- lines(x=xv, y=yv, lwd=1, col=tracecol, type="s")
- }
- }
-
- if(trace %in% c("both","row") )
- {
- for( i in rowInd )
- {
- if(!is.null(hline))
- {
- hline.vals <- scale01(hline, min.scale, max.scale)
- abline(h=i + hline, col=linecol, lty=2)
- }
- yv <- rep(i, ncol(x.scaled)) + x.scaled[i,] - 0.5
- yv <- rev(c(yv[1], yv))
- xv <- length(yv):1-0.5
- lines(x=xv, y=yv, lwd=1, col=tracecol, type="s")
- }
- }
+ if(!missing(cellnote))
+ text(x=c(row(cellnote)),
+ y=c(col(cellnote)),
+ labels=c(cellnote),
+ col=notecol,
+ cex=notecex)
+ ## the two dendrograms :
+ par(mar = c(margins[1], 0, 0, 0))
+ if( dendrogram %in% c("both","row") )
+ {
+ plot(ddr, horiz = TRUE, axes = FALSE, yaxs = "i", leaflab = "none")
+ }
+ else
+ plot.new()
- if(!missing(cellnote))
- text(x=c(row(cellnote)),
- y=c(col(cellnote)),
- labels=c(cellnote),
- col=notecol,
- cex=notecex)
+ par(mar = c(0, 0, if(!is.null(main)) 5 else 0, margins[2]))
- ## the two dendrograms :
- par(mar = c(margins[1], 0, 0, 0))
- if( dendrogram %in% c("both","row") )
- {
- plot(ddr, horiz = TRUE, axes = FALSE, yaxs = "i", leaflab = "none")
- }
- else
- plot.new()
+ if( dendrogram %in% c("both","column") )
+ {
+ plot(ddc, axes = FALSE, xaxs = "i", leaflab = "none")
+ }
+ else
+ plot.new()
- par(mar = c(0, 0, if(!is.null(main)) 5 else 0, margins[2]))
+ ## title
+ if(!is.null(main)) title(main, cex.main = 1.5*op[["cex.main"]])
- if( dendrogram %in% c("both","column") )
- {
- plot(ddc, axes = FALSE, xaxs = "i", leaflab = "none")
- }
- else
- plot.new()
+ ## Add the color-key
+ if(key)
+ {
+ par(mar = c(5, 4, 2, 1), cex=0.75)
+ tmpbreaks <- breaks
- ## title
- if(!is.null(main)) title(main, cex.main = 1.5*op[["cex.main"]])
+ if(symkey)
+ {
+ max.raw <- max(abs(c(x,breaks)),na.rm=TRUE)
+ min.raw <- -max.raw
+ tmpbreaks[1] <- -max(abs(x))
+ tmpbreaks[length(tmpbreaks)] <- max(abs(x))
+ }
+ 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)
+ }
- ## Add the color-key
- if(key)
- {
- par(mar = c(5, 4, 2, 1), cex=0.75)
+ z <- seq(min.raw, max.raw, length=length(col))
+ image(z=matrix(z, ncol=1),
+ col=col, breaks=tmpbreaks,
+ xaxt="n", yaxt="n")
- if(symkey)
- {
- max.raw <- max(abs(x),na.rm=TRUE)
- min.raw <- -max.raw
- }
- 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)
- }
+ par(usr=c(0,1,0,1))
+ lv <- pretty(breaks)
+ xv <- scale01(as.numeric(lv), min.raw, max.raw)
+ axis(1, at=xv, labels=lv)
+ if(scale=="row")
+ mtext(side=1,"Row Z-Score", line=2)
+ else if(scale=="column")
+ mtext(side=1,"Column Z-Score", line=2)
+ else
+ mtext(side=1,"Value", line=2)
- z <- seq(min.raw,max.raw,length=length(col))
- image(z=matrix(z, ncol=1),
- col=col, breaks=breaks,
- xaxt="n", yaxt="n" )
+ if(density.info=="density")
+ {
+ ## Experimental : also plot density of data
+ dens <- density(x, adjust=densadj, na.rm=TRUE)
+ omit <- dens$x < min(breaks) | dens$x > max(breaks)
+ dens$x <- dens$x[-omit]
+ dens$y <- dens$y[-omit]
+ dens$x <- scale01(dens$x,min.raw,max.raw)
+ lines(dens$x, dens$y / max(dens$y) * 0.95, col=denscol, lwd=1)
+ axis(2, at=pretty(dens$y)/max(dens$y) * 0.95, pretty(dens$y) )
+ title("Color Key\nand Density Plot")
+ par(cex=0.5)
+ mtext(side=2,"Density", line=2)
+ }
+ else if(density.info=="histogram")
+ {
+ h <- hist(x, plot=FALSE, breaks=breaks)
+ hx <- scale01(breaks,min.raw,max.raw)
+ hy <- c(h$counts, h$counts[length(h$counts)])
+ lines(hx, hy/max(hy)*0.95, lwd=1, type="s", col=denscol)
+ axis(2, at=pretty(hy)/max(hy) * 0.95, pretty(hy) )
+ title("Color Key\nand Histogram")
+ par(cex=0.5)
+ mtext(side=2,"Count", line=2)
+ }
+ else
+ title("Color Key")
- par(usr=c(0,1,0,1))
- lv <- pretty(breaks)
- xv <- scale01(as.numeric(lv), min.raw, max.raw)
- axis(1, at=xv, labels=lv)
- if(scale=="row")
- mtext(side=1,"Row Z-Score", line=2)
- else if(scale=="column")
- mtext(side=1,"Column Z-Score", line=2)
- else
- mtext(side=1,"Value", line=2)
+ }
+ else
+ plot.new()
- if(density.info=="density")
- {
- # Experimental : also plot density of data
- dens <- density(x, adjust=densadj, na.rm=TRUE)
- omit <- dens$x < min(breaks) | dens$x > max(breaks)
- dens$x <- dens$x[-omit]
- dens$y <- dens$y[-omit]
- dens$x <- scale01(dens$x,min.raw,max.raw)
- lines(dens$x, dens$y / max(dens$y) * 0.95, col=denscol, lwd=1)
- axis(2, at=pretty(dens$y)/max(dens$y) * 0.95, pretty(dens$y) )
- title("Color Key\nand Density Plot")
- par(cex=0.5)
- mtext(side=2,"Density", line=2)
- }
- else if(density.info=="histogram")
- {
- h <- hist(x, plot=FALSE, breaks=breaks)
- hx <- scale01(breaks,min.raw,max.raw)
- hy <- c(h$counts, h$counts[length(h$counts)])
- lines(hx, hy/max(hy)*0.95, lwd=1, type="s", col=denscol)
- axis(2, at=pretty(hy)/max(hy) * 0.95, pretty(hy) )
- title("Color Key\nand Histogram")
- par(cex=0.5)
- mtext(side=2,"Count", line=2)
- }
- else
- title("Color Key")
+ ## Create a table showing how colors match to (transformed) data ranges
+ retval$colorTable <- data.frame(
+ low=retval$breaks[-length(retval$breaks)],
+ high=retval$breaks[-1],
+ color=retval$col
+ )
- }
- else
- plot.new()
-
- invisible(list(rowInd = rowInd, colInd = colInd))
+
+ invisible( retval )
}
Modified: trunk/gplots/man/heatmap.2.Rd
===================================================================
--- trunk/gplots/man/heatmap.2.Rd 2009-05-08 21:27:55 UTC (rev 1316)
+++ trunk/gplots/man/heatmap.2.Rd 2009-05-08 21:55:05 UTC (rev 1317)
@@ -1,85 +1,92 @@
\name{heatmap.2}
\alias{heatmap.2}
-\title{ Draw a Heat Map }
+\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
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.
+
+ This heatmap provides a number of extensions to the standard R
+ \code{\link[stats]{heatmap}} function.
}
\usage{
heatmap.2 (x,
- # dendrogram control
- Rowv = TRUE,
- Colv=if(symm)"Rowv" else TRUE,
- distfun = dist,
- hclustfun = hclust,
- dendrogram = c("both","row","column","none"),
- symm = FALSE,
+ # dendrogram control
+ Rowv = TRUE,
+ Colv=if(symm)"Rowv" else TRUE,
+ distfun = dist,
+ hclustfun = hclust,
+ dendrogram = c("both","row","column","none"),
+ symm = FALSE,
- # data scaling
- scale = c("none","row", "column"),
- na.rm=TRUE,
+ # data scaling
+ scale = c("none","row", "column"),
+ na.rm=TRUE,
- # image plot
- revC = identical(Colv, "Rowv"),
- add.expr,
- breaks,
- col="heat.colors",
+ # image plot
+ revC = identical(Colv, "Rowv"),
+ add.expr,
- # block sepration
- colsep,
- rowsep,
- sepcolor="white",
- sepwidth=c(0.05,0.05),
+ # mapping data to colors
+ breaks,
+ symbreaks=min(x < 0, na.rm=TRUE) || scale!="none",
- # cell labeling
- cellnote,
- notecex=1.0,
- notecol="cyan",
- na.color=par("bg"),
+ # colors
+ col="heat.colors",
- # level trace
- trace=c("column","row","both","none"),
- tracecol="cyan",
- hline=median(breaks),
- vline=median(breaks),
- linecol=tracecol,
+ # block sepration
+ colsep,
+ rowsep,
+ sepcolor="white",
+ sepwidth=c(0.05,0.05),
- # Row/Column Labeling
- margins = c(5, 5),
- ColSideColors,
- RowSideColors,
- cexRow = 0.2 + 1/log10(nr),
- cexCol = 0.2 + 1/log10(nc),
- labRow = NULL,
- labCol = NULL,
+ # cell labeling
+ cellnote,
+ notecex=1.0,
+ notecol="cyan",
+ na.color=par("bg"),
- # color key + density info
- key = TRUE,
- keysize = 1.5,
- density.info=c("histogram","density","none"),
- denscol=tracecol,
- #symkey = TRUE, # should be something like
- symkey = min(x < 0, na.rm=TRUE),
- densadj = 0.25,
+ # level trace
+ trace=c("column","row","both","none"),
+ tracecol="cyan",
+ hline=median(breaks),
+ vline=median(breaks),
+ linecol=tracecol,
- # plot labels
- main = NULL,
- xlab = NULL,
- ylab = NULL,
+ # Row/Column Labeling
+ margins = c(5, 5),
+ ColSideColors,
+ RowSideColors,
+ cexRow = 0.2 + 1/log10(nr),
+ cexCol = 0.2 + 1/log10(nc),
+ labRow = NULL,
+ labCol = NULL,
- # plot layout
- lmat = NULL,
- lhei = NULL,
- lwid = NULL,
+ # color key + density info
+ key = TRUE,
+ keysize = 1.5,
+ density.info=c("histogram","density","none"),
+ denscol=tracecol,
+ symkey = min(x < 0, na.rm=TRUE) || symbreaks,
+ densadj = 0.25,
- # extras
- ...
- )
- }
+ # plot labels
+ main = NULL,
+ xlab = NULL,
+ ylab = NULL,
+
+ # plot layout
+ lmat = NULL,
+ lhei = NULL,
+ lwid = NULL,
+
+ # extras
+ ...
+ )
+ }
\arguments{
% Dendogram Control
\item{x}{numeric matrix of the values to be plotted. }
@@ -121,6 +128,9 @@
splitting points for binning \code{x} into colors, or a integer
number of break points to be used, in which case the break points
will be spaced equally between \code{min(x)} and \code{max(x)}.}
+ \item{symbreaks}{Boolean indicating whether breaks should be
+ made symmetric about 0. Defaults to \code{TRUE} if the data includes
+ negative values, and to \code{FALSE} otherwise.}
\item{col}{colors used for the image. Defaults to heat colors
(\code{heat.colors}).}
% block separation
@@ -178,7 +188,8 @@
display specified by \code{density.info}, defaults to the same value
as \code{tracecol}.}
\item{symkey}{Boolean indicating whether the color key should be
- made symmetric about 0. Defaults to \code{TRUE}.}
+ made symmetric about 0. Defaults to \code{TRUE} if the data includes
+ negative values, and to \code{FALSE} otherwise.}
\item{densadj}{Numeric scaling value for tuning the kernel width when
a density plot is drawn on the color key. (See the \code{adjust}
parameter for the \code{density} function for details.) Defaults to
@@ -244,9 +255,26 @@
}
\value{
Invisibly, a list with components
- \item{rowInd}{\bold{r}ow index permutation vector as returned by
+ \item{rowInd}{row index permutation vector as returned by
\code{\link{order.dendrogram}}.}
- \item{colInd}{\bold{c}olumn index permutation vector.}
+ \item{colInd}{column index permutation vector.}
+ \item{call}{the matched call}
+ \item{rowMeans, rowSDs}{mean and standard deviation of each row: only
+ present if \code{scale="row"}}
+ \item{colMeans, colSDs}{mean and standard deviation of each column: only
+ present if \code{scale="column"}}
+ \item{carpet}{reordered and scaled 'x' values used generate the main
+ 'carpet'}
+ \item{rowDendrogram}{row dendrogram, if present}
+ \item{colDendrogram}{column dendrogram, if present}
+ \item{breaks}{values used for color break points}
+ \item{col}{colors used}
+ \item{vline}{center-line value used for column trace, present only if
+ \code{trace="both"} or \code{trace="column"} }
+ \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}
}
\author{Andy Liaw, original; R. Gentleman, M. Maechler, W. Huber,
G. Warnes, revisions.}
@@ -260,6 +288,9 @@
rc <- rainbow(nrow(x), start=0, end=.3)
cc <- rainbow(ncol(x), start=0, end=.3)
+ ##
+ ## demonstrate the effect of row and column dendogram options
+ ##
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.
@@ -267,22 +298,45 @@
heatmap.2(x, keysize=2) ## default - dendrogram plotted and reordering done.
-
heatmap.2(x, Rowv=FALSE, dendrogram="both") ## generate warning!
heatmap.2(x, Rowv=NULL, dendrogram="both") ## generate warning!
heatmap.2(x, Colv=FALSE, dendrogram="both") ## generate warning!
+ ##
+ ## Show effect of z-score scaling within columns, blue-red color scale
+ ##
+ hv <- heatmap.2(x, col=bluered, scale="column", tracecol="#303030")
+ ###
+ ## Look at the return values
+ ###
+ names(hv)
+ ## Show the mapping of z-score values to color bins
+ hv$colorTable
- hv <- heatmap.2(x, col=cm.colors(256), scale="column",
+ ## Extract the range associated with white
+ hv$colorTable[hv$colorTable[,"color"]=="#FFFFFF",]
+
+ ## Determine the original data values that map to white
+ whiteBin <- unlist(hv$colorTable[hv$colorTable[,"color"]=="#FFFFFF",1:2])
+ rbind(whiteBin[1] * hv$colSDs + hv$colMeans,
+ whiteBin[2] * hv$colSDs + hv$colMeans )
+ ##
+ ## 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\")",
tracecol="green", density="density")
+ ## Note that the breakpoints are now symmetric about 0
- str(hv) # the two re-ordering index vectors
+
+
+
+
%% want example using the `add.exp' argument!
data(attitude)
Modified: trunk/gplots/tests/heatmap2Test.Rout.save
===================================================================
--- trunk/gplots/tests/heatmap2Test.Rout.save 2009-05-08 21:27:55 UTC (rev 1316)
+++ trunk/gplots/tests/heatmap2Test.Rout.save 2009-05-08 21:55:05 UTC (rev 1317)
@@ -1,6 +1,6 @@
-R version 2.6.0 (2007-10-03)
-Copyright (C) 2007 The R Foundation for Statistical Computing
+R version 2.9.0 (2009-04-17)
+Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -18,6 +18,9 @@
> library(gplots)
Loading required package: gtools
Loading required package: gdata
+Loading required package: caTools
+Loading required package: bitops
+Loading required package: grid
Attaching package: 'gplots'
@@ -112,8 +115,108 @@
+ tracecol="green", density="density")
>
> str(hv) # the two re-ordering index vectors
-List of 2
- $ rowInd: int [1:32] 31 17 16 15 5 25 29 24 7 6 ...
- $ colInd: int [1:11] 2 9 8 11 6 5 10 7 1 4 ...
+List of 12
+ $ rowInd : int [1:32] 31 17 16 15 5 25 29 24 7 6 ...
+ $ colInd : int [1:11] 2 9 8 11 6 5 10 7 1 4 ...
+ $ call : language heatmap.2(x = x, scale = "column", col = cm.colors(256), tracecol = "green", margins = c(5, 10), ColSideColors = cc, RowSideColors = rc, ...
+ $ colMeans : Named num [1:11] 6.188 0.406 0.438 2.812 3.217 ...
+ ..- attr(*, "names")= chr [1:11] "cyl" "am" "vs" "carb" ...
+ $ colSDs : Named num [1:11] 1.786 0.499 0.504 1.615 0.978 ...
+ ..- attr(*, "names")= chr [1:11] "cyl" "am" "vs" "carb" ...
+ $ carpet : num [1:11, 1:32] 1.015 1.19 -0.868 3.212 0.361 ...
+ ..- attr(*, "dimnames")=List of 2
+ .. ..$ : chr [1:11] "cyl" "am" "vs" "carb" ...
+ .. ..$ : chr [1:32] "Maserati Bora" "Chrysler Imperial" "Lincoln Continental" "Cadillac Fleetwood" ...
+ $ rowDendrogram: ..--[dendrogram w/ 2 branches and 32 members at h = 425, midpoint = 8.58, value = 1267]
+ .. |--[dendrogram w/ 2 branches and 9 members at h = 215, midpoint = 1.84, value = 552]
+ .. | |--leaf "Maserati Bora" ( value.Maserati Bora = 63.2 )
+ .. | `--[dendrogram w/ 2 branches and 8 members at h = 135, midpoint = 2.69, value = 489]
+ .. | |--[dendrogram w/ 2 branches and 3 members at h = 40.8, midpoint = 0.75, value = 198]
+ .. | | |--leaf "Chrysler Imperial" ( value.Chrysler Imperial = 66 )
+ .. | | `--[dendrogram w/ 2 branches and 2 members at h = 15.6, midpoint = 0.5, value = 132]
+ .. | | |--leaf "Lincoln Continental" ( value.Lincoln Continental = 66 )
+ .. | | `--leaf "Cadillac Fleetwood" ( value.Cadillac Fleetwood = 66.2 )
+ .. | `--[dendrogram w/ 2 branches and 5 members at h = 102, midpoint = 1.62, value = 290]
+ .. | |--[dendrogram w/ 2 branches and 2 members at h = 40, midpoint = 0.5, value = 111]
+ .. | | |--leaf "Hornet Sportabout" ( value.Hornet Sportabout = 53.7 )
+ .. | | `--leaf "Pontiac Firebird" ( value.Pontiac Firebird = 57.4 )
+ .. | `--[dendrogram w/ 2 branches and 3 members at h = 21.3, midpoint = 0.75, value = 179]
+ .. | |--leaf "Ford Pantera L" ( value.Ford Pantera L = 61 )
+ .. | `--[dendrogram w/ 2 branches and 2 members at h = 10.1, midpoint = 0.5, value = 118]
+ .. | |--leaf "Camaro Z28" ( value.Camaro Z28 = 58.8 )
+ .. | `--leaf "Duster 360" ( value.Duster 360 = 59.7 )
+ .. `--[dendrogram w/ 2 branches and 23 members at h = 262, midpoint = 6.33, value = 716]
+ .. |--[dendrogram w/ 2 branches and 7 members at h = 103, midpoint = 2.06, value = 306]
+ .. | |--[dendrogram w/ 2 branches and 2 members at h = 33.6, midpoint = 0.5, value = 73.8]
+ .. | | |--leaf "Valiant" ( value.Valiant = 35.0 )
+ .. | | `--leaf "Hornet 4 Drive" ( value.Hornet 4 Drive = 38.7 )
+ .. | `--[dendrogram w/ 2 branches and 5 members at h = 51.8, midpoint = 1.62, value = 233]
+ .. | |--[dendrogram w/ 2 branches and 2 members at h = 14.0, midpoint = 0.5, value = 93.2]
+ .. | | |--leaf "AMC Javelin" ( value.AMC Javelin = 46 )
+ .. | | `--leaf "Dodge Challenger" ( value.Dodge Challenger = 47.2 )
+ .. | `--[dendrogram w/ 2 branches and 3 members at h = 2.14, midpoint = 0.75, value = 139]
+ .. | |--leaf "Merc 450SLC" ( value.Merc 450SLC = 46.4 )
+ .. | `--[dendrogram w/ 2 branches and 2 members at h = 0.983, midpoint = 0.5, value = 93]
+ .. | |--leaf "Merc 450SE" ( value.Merc 450SE = 46.4 )
+ .. | `--leaf "Merc 450SL" ( value.Merc 450SL = 46.5 )
+ .. `--[dendrogram w/ 2 branches and 16 members at h = 142, midpoint = 3.59, value = 409]
+ .. |--[dendrogram w/ 2 branches and 4 members at h = 14.8, midpoint = 0.875, value = 75]
+ .. | |--leaf "Honda Civic" ( value.Honda Civic = 17.7 )
+ .. | `--[dendrogram w/ 2 branches and 3 members at h = 10.4, midpoint = 0.75, value = 57.2]
+ .. | |--leaf "Toyota Corolla" ( value.Toyota Corolla = 18.8 )
+ .. | `--[dendrogram w/ 2 branches and 2 members at h = 5.15, midpoint = 0.5, value = 38.4]
+ .. | |--leaf "Fiat X1-9" ( value.Fiat X1-9 = 18.9 )
+ .. | `--leaf "Fiat 128" ( value.Fiat 128 = 19.4 )
+ .. `--[dendrogram w/ 2 branches and 12 members at h = 113, midpoint = 2.30, value = 334]
+ .. |--leaf "Ferrari Dino" ( value.Ferrari Dino = 34.5 )
+ .. `--[dendrogram w/ 2 branches and 11 members at h = 74.4, midpoint = 3.61, value = 300]
+ .. |--[dendrogram w/ 2 branches and 5 members at h = 64.9, midpoint = 1.25, value = 148]
+ .. | |--leaf "Merc 240D" ( value.Merc 240D = 24.6 )
+ .. | `--[dendrogram w/ 2 branches and 4 members at h = 15.7, midpoint = 1.5, value = 124]
+ .. | |--[dendrogram w/ 2 branches and 2 members at h = 0.615, midpoint = 0.5, value = 59.9]
+ .. | | |--leaf "Mazda RX4" ( value.Mazda RX4 = 29.9 )
+ .. | | `--leaf "Mazda RX4 Wag" ( value.Mazda RX4 Wag = 30 )
+ .. | `--[dendrogram w/ 2 branches and 2 members at h = 1.52, midpoint = 0.5, value = 63.6]
+ .. | |--leaf "Merc 280C" ( value.Merc 280C = 31.8 )
+ .. | `--leaf "Merc 280" ( value.Merc 280 = 31.9 )
+ .. `--[dendrogram w/ 2 branches and 6 members at h = 50.1, midpoint = 0.969, value = 152]
+ .. |--leaf "Lotus Europa" ( value.Lotus Europa = 24.9 )
+ .. `--[dendrogram w/ 2 branches and 5 members at h = 33.2, midpoint = 0.938, value = 127]
+ .. |--leaf "Merc 230" ( value.Merc 230 = 27.2 )
+ .. `--[dendrogram w/ 2 branches and 4 members at h = 20.7, midpoint = 0.875, value = 99.5]
+ .. |--leaf "Volvo 142E" ( value.Volvo 142E = 26.3 )
+ .. `--[dendrogram w/ 2 branches and 3 members at h = 13.1, midpoint = 0.75, value = 73.3]
+ .. |--leaf "Datsun 710" ( value.Datsun 710 = 23.6 )
+ .. `--[dendrogram w/ 2 branches and 2 members at h = 8.65, midpoint = 0.5, value = 49.7]
+ .. |--leaf "Porsche 914-2" ( value.Porsche 914-2 = 24.8 )
+ .. `--leaf "Toyota Corona" ( value.Toyota Corona = 24.9 )
+ $ colDendrogram: ..--[dendrogram w/ 2 branches and 11 members at h = 1475, midpoint = 7, value = 436]
+ .. |--[dendrogram w/ 2 branches and 9 members at h = 116, midpoint = 4.5, value = 58.3]
+ .. | |--[dendrogram w/ 2 branches and 7 members at h = 34.8, midpoint = 1.5, value = 20.3]
+ .. | | |--leaf "cyl" ( value.cyl = 6.19 )
+ .. | | `--[dendrogram w/ 2 branches and 6 members at h = 18.9, midpoint = 2, value = 14.2]
+ .. | | |--[dendrogram w/ 2 branches and 2 members at h = 3.61, midpoint = 0.5, value = 0.844]
+ .. | | | |--leaf "am" ( value.am = 0.406 )
+ .. | | | `--leaf "vs" ( value.vs = 0.438 )
+ .. | | `--[dendrogram w/ 2 branches and 4 members at h = 10.7, midpoint = 1.5, value = 13.3]
+ .. | | |--[dendrogram w/ 2 branches and 2 members at h = 8.6, midpoint = 0.5, value = 6.03]
+ .. | | | |--leaf "carb" ( value.carb = 2.81 )
+ .. | | | `--leaf "wt" ( value.wt = 3.22 )
+ .. | | `--[dendrogram w/ 2 branches and 2 members at h = 2.98, midpoint = 0.5, value = 7.28]
+ .. | | |--leaf "drat" ( value.drat = 3.6 )
+ .. | | `--leaf "gear" ( value.gear = 3.69 )
+ .. | `--[dendrogram w/ 2 branches and 2 members at h = 33.3, midpoint = 0.5, value = 37.9]
+ .. | |--leaf "qsec" ( value.qsec = 17.8 )
+ .. | `--leaf "mpg" ( value.mpg = 20.1 )
+ .. `--[dendrogram w/ 2 branches and 2 members at h = 657, midpoint = 0.5, value = 377]
+ .. |--leaf "hp" ( value.hp = 147 )
+ .. `--leaf "disp" ( value.disp = 231 )
+ $ breaks : num [1:257] -3.21 -3.19 -3.16 -3.14 -3.11 ...
+ $ col : chr [1:256] "#80FFFFFF" "#80FFFFFF" "#81FFFFFF" "#82FFFFFF" ...
+ $ vline : num 0
+ $ colorTable :'data.frame': 256 obs. of 3 variables:
+ ..$ low : num [1:256] -3.21 -3.19 -3.16 -3.14 -3.11 ...
+ ..$ high : num [1:256] -3.19 -3.16 -3.14 -3.11 -3.09 ...
+ ..$ color: Factor w/ 254 levels "#80FFFFFF","#81FFFFFF",..: 1 1 2 3 4 5 6 7 8 9 ...
>
>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
