Thread: [R-gregmisc-users] SF.net SVN: r-gregmisc:[1323] trunk/gplots/R/heatmap.2.R
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From: <wa...@us...> - 2009-05-08 22:51:25
|
Revision: 1323
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1323&view=rev
Author: warnes
Date: 2009-05-08 22:51:07 +0000 (Fri, 08 May 2009)
Log Message:
-----------
heatmap.2: handle NA for RowV or ColV the same way as NULL
Modified Paths:
--------------
trunk/gplots/R/heatmap.2.R
Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R 2009-05-08 22:35:25 UTC (rev 1322)
+++ trunk/gplots/R/heatmap.2.R 2009-05-08 22:51:07 UTC (rev 1323)
@@ -103,9 +103,9 @@
## key=FALSE
## }
- if ( is.null(Rowv) )
+ if ( is.null(Rowv) || is.na(Rowv) )
Rowv <- FALSE
- if ( is.null(Colv) )
+ if ( is.null(Colv) || is.na(Colv) )
Colv <- FALSE
else if( Colv=="Rowv" && !isTRUE(Rowv) )
Colv <- FALSE
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From: <wa...@us...> - 2009-10-22 20:31:58
|
Revision: 1362
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1362&view=rev
Author: warnes
Date: 2009-10-22 20:31:50 +0000 (Thu, 22 Oct 2009)
Log Message:
-----------
Fix transposed display of data (but not labels) in heatmap.2 when symm=TRUE
Modified Paths:
--------------
trunk/gplots/R/heatmap.2.R
Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R 2009-10-12 13:26:35 UTC (rev 1361)
+++ trunk/gplots/R/heatmap.2.R 2009-10-22 20:31:50 UTC (rev 1362)
@@ -354,11 +354,11 @@
}
## draw the main carpet
par(mar = c(margins[1], 0, 0, margins[2]))
- if(!symm || scale != "none")
- {
- x <- t(x)
- cellnote <- t(cellnote)
- }
+ #if(scale != "none" || !symm)
+ # {
+ # x <- t(x)
+ # cellnote <- t(cellnote)
+ # }
if(revC)
{ ## x columns reversed
iy <- nr:1
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From: <wa...@us...> - 2009-10-22 20:53:19
|
Revision: 1364
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1364&view=rev
Author: warnes
Date: 2009-10-22 20:53:11 +0000 (Thu, 22 Oct 2009)
Log Message:
-----------
Fixed typo in bug fix.
Modified Paths:
--------------
trunk/gplots/R/heatmap.2.R
Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R 2009-10-22 20:37:49 UTC (rev 1363)
+++ trunk/gplots/R/heatmap.2.R 2009-10-22 20:53:11 UTC (rev 1364)
@@ -356,8 +356,8 @@
par(mar = c(margins[1], 0, 0, margins[2]))
#if(scale != "none" || !symm)
# {
- # x <- t(x)
- # cellnote <- t(cellnote)
+ x <- t(x)
+ cellnote <- t(cellnote)
# }
if(revC)
{ ## x columns reversed
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From: <wa...@us...> - 2010-12-13 16:44:24
|
Revision: 1463
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1463&view=rev
Author: warnes
Date: 2010-12-13 16:44:17 +0000 (Mon, 13 Dec 2010)
Log Message:
-----------
Correct error that arises when data includes NA values, identified by Melissa Key
Modified Paths:
--------------
trunk/gplots/R/heatmap.2.R
Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R 2010-11-12 19:14:06 UTC (rev 1462)
+++ trunk/gplots/R/heatmap.2.R 2010-12-13 16:44:17 UTC (rev 1463)
@@ -493,8 +493,8 @@
{
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))
+ tmpbreaks[1] <- -max(abs(x), na.rm=TRUE)
+ tmpbreaks[length(tmpbreaks)] <- max(abs(x), na.rm=TRUE)
}
else
{
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From: <wa...@us...> - 2014-04-04 21:32:57
|
Revision: 1778
http://sourceforge.net/p/r-gregmisc/code/1778
Author: warnes
Date: 2014-04-04 21:32:51 +0000 (Fri, 04 Apr 2014)
Log Message:
-----------
Fix handling of row trace (hline). Bug report and patch provided by Ilia Kats.
Modified Paths:
--------------
trunk/gplots/R/heatmap.2.R
Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R 2014-03-19 10:04:49 UTC (rev 1777)
+++ trunk/gplots/R/heatmap.2.R 2014-04-04 21:32:51 UTC (rev 1778)
@@ -86,9 +86,9 @@
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)
@@ -115,8 +115,8 @@
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")
@@ -141,10 +141,10 @@
dendrogram <- "column"
else
dedrogram <- "none"
-
+
warning("Discrepancy: Rowv is FALSE, while dendrogram is `",
dendrogram, "'. Omitting row dendogram.")
-
+
}
}
@@ -157,13 +157,13 @@
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)
@@ -175,32 +175,32 @@
if(inherits(Rowv, "dendrogram"))
{
ddr <- Rowv ## use Rowv 'as-is', when it is dendrogram
- rowInd <- order.dendrogram(ddr)
+ rowInd <- order.dendrogram(ddr)
}
else if (is.integer(Rowv))
{ ## Compute dendrogram and do reordering based on given vector
hcr <- hclustfun(distfun(x))
ddr <- as.dendrogram(hcr)
ddr <- reorder(ddr, Rowv)
-
+
rowInd <- order.dendrogram(ddr)
if(nr != length(rowInd))
stop("row dendrogram ordering gave index of wrong length")
}
- else if (isTRUE(Rowv))
+ else if (isTRUE(Rowv))
{ ## If TRUE, compute dendrogram and do reordering based on rowMeans
Rowv <- rowMeans(x, na.rm = na.rm)
hcr <- hclustfun(distfun(x))
ddr <- as.dendrogram(hcr)
ddr <- reorder(ddr, Rowv)
-
+
rowInd <- order.dendrogram(ddr)
if(nr != length(rowInd))
stop("row dendrogram ordering gave index of wrong length")
} else {
rowInd <- nr:1
}
-
+
## if( dendrogram %in% c("both","column") )
## {
if(inherits(Colv, "dendrogram"))
@@ -247,7 +247,7 @@
retval$colInd <- colInd
retval$call <- match.call()
-
+
## reorder x & cellnote
x <- x[rowInd, colInd]
x.unscaled <- x
@@ -281,10 +281,10 @@
{
if( missing(col) || is.function(col) )
breaks <- 16
- else
+ else
breaks <- length(col)+1
}
-
+
if(length(breaks)==1)
{
if(!symbreaks)
@@ -308,7 +308,7 @@
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)
@@ -319,7 +319,7 @@
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)")
@@ -336,7 +336,7 @@
lmat[is.na(lmat)] <- 0
}
-
+
if(length(lhei) != nrow(lmat))
stop("lhei must have length = nrow(lmat) = ", nrow(lmat))
@@ -386,7 +386,7 @@
retval$colDendrogram <- ddc
retval$breaks <- breaks
retval$col <- col
-
+
## fill 'na' positions with na.color
if(!invalid(na.color) & any(is.na(x)))
{
@@ -421,7 +421,7 @@
y=par("usr")[3] - (1.0 + offsetCol) * strheight("M"),
labels=labCol,
##pos=1,
- adj=adjCol,
+ adj=adjCol,
cex=cexCol,
srt=srtCol)
par(xpd=xpd.orig)
@@ -487,7 +487,7 @@
xright=nrow(x)+1, ytop = (ncol(x)+1-rsep)-0.5 - sepwidth[2],
lty=1, lwd=1, col=sepcolor, border=sepcolor)
-
+
## show traces
min.scale <- min(breaks)
max.scale <- max(breaks)
@@ -510,7 +510,7 @@
}
}
-
+
if(trace %in% c("both","row") )
{
retval$hline <- hline
@@ -519,7 +519,7 @@
{
if(!is.null(hline))
{
- abline(h=i + hline, col=linecol, lty=2)
+ abline(h=i - 0.5 + hline.vals, col=linecol, lty=2)
}
yv <- rep(i, ncol(x.scaled)) + x.scaled[i,] - 0.5
yv <- rev(c(yv[1], yv))
@@ -573,7 +573,7 @@
}
else
{
- min.raw <- min(x, na.rm=TRUE) ## Again, modified to use scaled
+ 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)
}
@@ -595,12 +595,11 @@
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)
+ 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")
@@ -610,7 +609,7 @@
else if(density.info=="histogram")
{
h <- hist(x, plot=FALSE, breaks=breaks)
- hx <- scale01(breaks,min.raw,max.raw)
+ hx <- scale01(breaks, min.raw, max.raw)
hy <- c(h$counts, h$counts[length(h$counts)])
lines(hx, hy/max(hy)*0.95, lwd=1, type="s", col=denscol)
axis(2, at=pretty(hy)/max(hy) * 0.95, pretty(hy) )
@@ -621,6 +620,30 @@
else
title("Color Key")
+
+ if(trace %in% c("both","column") )
+ {
+ vline.vals <- scale01(vline, min.raw, max.raw)
+ if(!is.null(vline))
+ {
+ abline(v=vline.vals, col=linecol, lty=2)
+ }
+ }
+
+
+ if(trace %in% c("both","row") )
+ {
+ hline.vals <- scale01(hline, min.raw, max.raw)
+ if(!is.null(hline))
+ {
+ abline(v=hline.vals, col=linecol, lty=2)
+
+ }
+ }
+
+
+
+
}
else
plot.new()
@@ -630,8 +653,8 @@
low=retval$breaks[-length(retval$breaks)],
high=retval$breaks[-1],
color=retval$col
- )
+ )
-
+
invisible( retval )
}
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From: <wa...@us...> - 2014-04-09 23:52:19
|
Revision: 1802
http://sourceforge.net/p/r-gregmisc/code/1802
Author: warnes
Date: 2014-04-09 23:52:17 +0000 (Wed, 09 Apr 2014)
Log Message:
-----------
Add padj=0.5 to better align margin labels.
Modified Paths:
--------------
trunk/gplots/R/heatmap.2.R
Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R 2014-04-05 21:08:41 UTC (rev 1801)
+++ trunk/gplots/R/heatmap.2.R 2014-04-09 23:52:17 UTC (rev 1802)
@@ -66,6 +66,12 @@
denscol=tracecol,
symkey = min(x < 0, na.rm=TRUE) || symbreaks,
densadj = 0.25,
+ key.title = NULL,
+ key.xlab = NULL,
+ key.ylab = NULL,
+ key.xtickfun = NULL,
+ key.ytickfun = NULL,
+ key.par=list(),
## plot labels
main = NULL,
@@ -562,7 +568,16 @@
## Add the color-key
if(key)
{
- par(mar = c(5, 4, 2, 1), cex=0.75)
+ mar <- c(5, 4, 2, 1)
+ if (!is.null(key.xlab) && is.na(key.xlab))
+ mar[1] <- 2
+ if (!is.null(key.ylab) && is.na(key.ylab))
+ mar[2] <- 2
+ if (!is.null(key.title) && is.na(key.title))
+ mar[3] <- 1
+ par(mar = mar, cex=0.75, mgp=c(2, 1, 0))
+ if (length(key.par) > 0)
+ do.call(par, key.par)
tmpbreaks <- breaks
if(symkey)
@@ -584,15 +599,26 @@
xaxt="n", yaxt="n")
par(usr=c(0,1,0,1))
- lv <- pretty(breaks)
- xv <- scale01(as.numeric(lv), min.raw, max.raw)
- axis(1, at=xv, labels=lv)
- if(scale=="row")
- mtext(side=1,"Row Z-Score", line=2)
- else if(scale=="column")
- mtext(side=1,"Column Z-Score", line=2)
- else
- mtext(side=1,"Value", line=2)
+ if (is.null(key.xtickfun)) {
+ lv <- pretty(breaks)
+ xv <- scale01(as.numeric(lv), min.raw, max.raw)
+ xargs <- list(at=xv, labels=lv)
+ } else {
+ xargs <- key.xtickfun()
+ }
+ xargs$side <- 1
+ do.call(axis, xargs)
+ if (is.null(key.xlab)) {
+ if(scale=="row")
+ key.xlab <- "Row Z-Score"
+ else if(scale=="column")
+ key.xlab <- "Column Z-Score"
+ else
+ key.xlab <- "Value"
+ }
+ if (!is.na(key.xlab)) {
+ mtext(side=1, key.xlab, line=par("mgp")[1], padj=0.5)
+ }
if(density.info=="density")
{
@@ -602,10 +628,22 @@
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")
+ if (is.null(key.ytickfun)) {
+ yargs <- list(at=pretty(dens$y)/max(dens$y) * 0.95, labels=pretty(dens$y))
+ } else {
+ yargs <- key.ytickfun()
+ }
+ yargs$side <- 2
+ do.call(axis, yargs)
+ if (is.null(key.title))
+ key.title <- "Color Key\nand Density Plot"
+ if (!is.na(key.title))
+ title(key.title)
par(cex=0.5)
- mtext(side=2,"Density", line=2)
+ if (is.null(key.ylab))
+ key.ylab <- "Density"
+ if (!is.na(key.ylab))
+ mtext(side=2,key.ylab, line=par("mgp")[1], padj=0.5)
}
else if(density.info=="histogram")
{
@@ -613,10 +651,22 @@
hx <- scale01(breaks, min.raw, max.raw)
hy <- c(h$counts, h$counts[length(h$counts)])
lines(hx, hy/max(hy)*0.95, lwd=1, type="s", col=denscol)
- axis(2, at=pretty(hy)/max(hy) * 0.95, pretty(hy) )
- title("Color Key\nand Histogram")
+ if (is.null(key.ytickfun)) {
+ yargs <- list(at=pretty(hy)/max(hy) * 0.95, labels=pretty(hy))
+ } else {
+ yargs <- key.ytickfun()
+ }
+ yargs$side <- 2
+ do.call(axis, yargs)
+ if (is.null(key.title))
+ key.title <- "Color Key\nand Histogram"
+ if (!is.na(key.title))
+ title(key.title)
par(cex=0.5)
- mtext(side=2,"Count", line=2)
+ if (is.null(key.ylab))
+ key.ylab <- "Count"
+ if (!is.na(key.ylab))
+ mtext(side=2,key.ylab, line=par("mgp")[1], padj=0.5)
}
else
title("Color Key")
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From: <wa...@us...> - 2014-06-05 17:21:17
|
Revision: 1817
http://sourceforge.net/p/r-gregmisc/code/1817
Author: warnes
Date: 2014-06-05 17:21:11 +0000 (Thu, 05 Jun 2014)
Log Message:
-----------
Check size of Rowv and Colv dendogram objects to ensure they matches data.
Modified Paths:
--------------
trunk/gplots/R/heatmap.2.R
Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R 2014-05-28 00:24:23 UTC (rev 1816)
+++ trunk/gplots/R/heatmap.2.R 2014-06-05 17:21:11 UTC (rev 1817)
@@ -183,6 +183,8 @@
{
ddr <- Rowv ## use Rowv 'as-is', when it is dendrogram
rowInd <- order.dendrogram(ddr)
+ if(length(rowInd)>nr || any(rowInd<1 | rowInd > nr ))
+ stop("Rowv dendrogram doesn't match size of x")
}
else if (is.integer(Rowv))
{ ## Compute dendrogram and do reordering based on given vector
@@ -214,6 +216,8 @@
{
ddc <- Colv ## use Colv 'as-is', when it is dendrogram
colInd <- order.dendrogram(ddc)
+ if(length(ColInd)>nr || any(colInd<1 | colInd > nc ))
+ stop("Colv dendrogram doesn't match size of x")
}
else if(identical(Colv, "Rowv")) {
if(nr != nc)
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From: <wa...@us...> - 2014-06-17 20:34:24
|
Revision: 1818
http://sourceforge.net/p/r-gregmisc/code/1818
Author: warnes
Date: 2014-06-17 20:34:17 +0000 (Tue, 17 Jun 2014)
Log Message:
-----------
Fix typo in heatmap.2() reported by Yuanhua Liu.
Modified Paths:
--------------
trunk/gplots/R/heatmap.2.R
Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R 2014-06-05 17:21:11 UTC (rev 1817)
+++ trunk/gplots/R/heatmap.2.R 2014-06-17 20:34:17 UTC (rev 1818)
@@ -147,7 +147,7 @@
if (is.logical(Colv) && (Colv))
dendrogram <- "column"
else
- dedrogram <- "none"
+ dendrogram <- "none"
warning("Discrepancy: Rowv is FALSE, while dendrogram is `",
dendrogram, "'. Omitting row dendogram.")
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From: <wa...@us...> - 2014-06-17 23:19:50
|
Revision: 1819
http://sourceforge.net/p/r-gregmisc/code/1819
Author: warnes
Date: 2014-06-17 23:19:46 +0000 (Tue, 17 Jun 2014)
Log Message:
-----------
Allow user to specify function used to reorder based on the dendogram
via a new 'reorderfun' argument. Suggested by Yuanhua Liu.
Modified Paths:
--------------
trunk/gplots/R/heatmap.2.R
Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R 2014-06-17 20:34:17 UTC (rev 1818)
+++ trunk/gplots/R/heatmap.2.R 2014-06-17 23:19:46 UTC (rev 1819)
@@ -8,6 +8,7 @@
distfun = dist,
hclustfun = hclust,
dendrogram = c("both","row","column","none"),
+ reorderfun = function(d, w) reorder(d, w),
symm = FALSE,
## data scaling
@@ -109,13 +110,6 @@
"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
- ## }
-
if ( is.null(Rowv) || is.na(Rowv) )
Rowv <- FALSE
if ( is.null(Colv) || is.na(Colv) )
@@ -190,7 +184,7 @@
{ ## Compute dendrogram and do reordering based on given vector
hcr <- hclustfun(distfun(x))
ddr <- as.dendrogram(hcr)
- ddr <- reorder(ddr, Rowv)
+ ddr <- reorderfun(ddr, Rowv)
rowInd <- order.dendrogram(ddr)
if(nr != length(rowInd))
@@ -201,7 +195,7 @@
Rowv <- rowMeans(x, na.rm = na.rm)
hcr <- hclustfun(distfun(x))
ddr <- as.dendrogram(hcr)
- ddr <- reorder(ddr, Rowv)
+ ddr <- reorderfun(ddr, Rowv)
rowInd <- order.dendrogram(ddr)
if(nr != length(rowInd))
@@ -232,7 +226,7 @@
{## Compute dendrogram and do reordering based on given vector
hcc <- hclustfun(distfun(if(symm)x else t(x)))
ddc <- as.dendrogram(hcc)
- ddc <- reorder(ddc, Colv)
+ ddc <- reorderfun(ddc, Colv)
colInd <- order.dendrogram(ddc)
if(nc != length(colInd))
@@ -243,7 +237,7 @@
Colv <- colMeans(x, na.rm = na.rm)
hcc <- hclustfun(distfun(if(symm)x else t(x)))
ddc <- as.dendrogram(hcc)
- ddc <- reorder(ddc, Colv)
+ ddc <- reorderfun(ddc, Colv)
colInd <- order.dendrogram(ddc)
if(nc != length(colInd))
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From: <wa...@us...> - 2014-06-19 18:51:40
|
Revision: 1822
http://sourceforge.net/p/r-gregmisc/code/1822
Author: warnes
Date: 2014-06-19 18:51:32 +0000 (Thu, 19 Jun 2014)
Log Message:
-----------
Fix typo 'ColInd' --> 'colInd'.
Modified Paths:
--------------
trunk/gplots/R/heatmap.2.R
Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R 2014-06-19 18:36:19 UTC (rev 1821)
+++ trunk/gplots/R/heatmap.2.R 2014-06-19 18:51:32 UTC (rev 1822)
@@ -210,7 +210,7 @@
{
ddc <- Colv ## use Colv 'as-is', when it is dendrogram
colInd <- order.dendrogram(ddc)
- if(length(ColInd)>nr || any(colInd<1 | colInd > nc ))
+ if(length(colInd)>nr || any(colInd<1 | colInd > nc ))
stop("Colv dendrogram doesn't match size of x")
}
else if(identical(Colv, "Rowv")) {
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From: <wa...@us...> - 2014-06-30 19:26:24
|
Revision: 1823
http://sourceforge.net/p/r-gregmisc/code/1823
Author: warnes
Date: 2014-06-30 19:26:21 +0000 (Mon, 30 Jun 2014)
Log Message:
-----------
Fix typo in dendrogram size checking code.
Modified Paths:
--------------
trunk/gplots/R/heatmap.2.R
Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R 2014-06-19 18:51:32 UTC (rev 1822)
+++ trunk/gplots/R/heatmap.2.R 2014-06-30 19:26:21 UTC (rev 1823)
@@ -210,7 +210,7 @@
{
ddc <- Colv ## use Colv 'as-is', when it is dendrogram
colInd <- order.dendrogram(ddc)
- if(length(colInd)>nr || any(colInd<1 | colInd > nc ))
+ if(length(colInd)>nc || any(colInd<1 | colInd > nc ))
stop("Colv dendrogram doesn't match size of x")
}
else if(identical(Colv, "Rowv")) {
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From: <wa...@us...> - 2014-09-17 13:53:42
|
Revision: 1889
http://sourceforge.net/p/r-gregmisc/code/1889
Author: warnes
Date: 2014-09-17 13:53:34 +0000 (Wed, 17 Sep 2014)
Log Message:
-----------
key.title=NA was not being honored when density.info=NA.
Modified Paths:
--------------
trunk/gplots/R/heatmap.2.R
Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R 2014-09-16 18:11:13 UTC (rev 1888)
+++ trunk/gplots/R/heatmap.2.R 2014-09-17 13:53:34 UTC (rev 1889)
@@ -667,7 +667,8 @@
mtext(side=2,key.ylab, line=par("mgp")[1], padj=0.5)
}
else
- title("Color Key")
+ if (is.null(key.title))
+ title("Color Key")
if(trace %in% c("both","column") )
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|
From: <wa...@us...> - 2014-09-17 21:34:37
|
Revision: 1890
http://sourceforge.net/p/r-gregmisc/code/1890
Author: warnes
Date: 2014-09-17 21:34:28 +0000 (Wed, 17 Sep 2014)
Log Message:
-----------
heatmap.2 was not properly handling integer vectors for Rowv and Colv.
Modified Paths:
--------------
trunk/gplots/R/heatmap.2.R
Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R 2014-09-17 13:53:34 UTC (rev 1889)
+++ trunk/gplots/R/heatmap.2.R 2014-09-17 21:34:28 UTC (rev 1890)
@@ -114,8 +114,8 @@
Rowv <- FALSE
if ( is.null(Colv) || is.na(Colv) )
Colv <- FALSE
- else if( Colv=="Rowv" && !isTRUE(Rowv) )
- Colv <- FALSE
+ else if( all(Colv=="Rowv") )
+ Colv <- Rowv
if(length(di <- dim(x)) != 2 || !is.numeric(x))
@@ -135,8 +135,15 @@
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(Rowv) && !isTRUE(Rowv) )
+ ||
+ ( is.null(Rowv) )
+ )
+ &&
+ ( dendrogram %in% c("both","row") )
+ )
{
if (is.logical(Colv) && (Colv))
dendrogram <- "column"
@@ -151,8 +158,14 @@
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(Colv) && !isTRUE(Colv) )
+ ||
+ (is.null(Colv))
+ )
+ &&
+ ( dendrogram %in% c("both","column")) )
{
if (is.logical(Rowv) && (Rowv))
dendrogram <- "row"
@@ -182,9 +195,10 @@
}
else if (is.integer(Rowv))
{ ## Compute dendrogram and do reordering based on given vector
+ browser()
hcr <- hclustfun(distfun(x))
ddr <- as.dendrogram(hcr)
- ddr <- reorderfun(ddr, Rowv)
+ ddr <- reorderfun(ddr, Rowv)
rowInd <- order.dendrogram(ddr)
if(nr != length(rowInd))
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From: <wa...@us...> - 2015-04-23 18:49:30
|
Revision: 1940
http://sourceforge.net/p/r-gregmisc/code/1940
Author: warnes
Date: 2015-04-23 18:49:23 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
In heatmap.2() split calls to distfun() and hclustfun() into separate steps to make debugging easier
Modified Paths:
--------------
trunk/gplots/R/heatmap.2.R
Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R 2015-04-23 17:40:13 UTC (rev 1939)
+++ trunk/gplots/R/heatmap.2.R 2015-04-23 18:49:23 UTC (rev 1940)
@@ -198,7 +198,8 @@
else if (is.integer(Rowv))
{ ## Compute dendrogram and do reordering based on given vector
browser()
- hcr <- hclustfun(distfun(x))
+ distr <- distfun(x)
+ hcr <- hclustfun(distr)
ddr <- as.dendrogram(hcr)
ddr <- reorderfun(ddr, Rowv)
@@ -209,7 +210,8 @@
else if (isTRUE(Rowv))
{ ## If TRUE, compute dendrogram and do reordering based on rowMeans
Rowv <- rowMeans(x, na.rm = na.rm)
- hcr <- hclustfun(distfun(x))
+ distr <- distfun(x)
+ hcr <- hclustfun(distr)
ddr <- as.dendrogram(hcr)
ddr <- reorderfun(ddr, Rowv)
@@ -240,7 +242,8 @@
colInd <- rowInd
} else if(is.integer(Colv))
{## Compute dendrogram and do reordering based on given vector
- hcc <- hclustfun(distfun(if(symm)x else t(x)))
+ distc <- distfun(if(symm)x else t(x))
+ hcc <- hclustfun(distc)
ddc <- as.dendrogram(hcc)
ddc <- reorderfun(ddc, Colv)
@@ -251,7 +254,8 @@
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)))
+ distc <- distfun(if(symm)x else t(x))
+ hcc <- hclustfun(distc)
ddc <- as.dendrogram(hcc)
ddc <- reorderfun(ddc, Colv)
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|
|
From: <wa...@us...> - 2015-04-23 19:09:24
|
Revision: 1941
http://sourceforge.net/p/r-gregmisc/code/1941
Author: warnes
Date: 2015-04-23 19:09:17 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
Patch submitted by Ilia Kats:
- easily extract and plot subclusters from a big heatmap using the
same colorkey, by passing a dendgrogram of the subcluster together
with the full data matrix and, optionally, the breaks of the full
heatmap in order to obtain the same color scaling. This is useful if
one wants to plot several subclusters as different panels in a
paper, but maintain consistent color coding.
- Improves the behavior of the color key axis labels, as they now
honor par("cex") and par("cex.lab").
Modified Paths:
--------------
trunk/gplots/R/heatmap.2.R
Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R 2015-04-23 18:49:23 UTC (rev 1940)
+++ trunk/gplots/R/heatmap.2.R 2015-04-23 19:09:17 UTC (rev 1941)
@@ -194,6 +194,8 @@
rowInd <- order.dendrogram(ddr)
if(length(rowInd)>nr || any(rowInd<1 | rowInd > nr ))
stop("Rowv dendrogram doesn't match size of x")
+ if (length(rowInd) < nr)
+ nr <- length(rowInd)
}
else if (is.integer(Rowv))
{ ## Compute dendrogram and do reordering based on given vector
@@ -230,6 +232,8 @@
colInd <- order.dendrogram(ddc)
if(length(colInd)>nc || any(colInd<1 | colInd > nc ))
stop("Colv dendrogram doesn't match size of x")
+ if (length(colInd) < nc)
+ nc <- length(colInd)
}
else if(identical(Colv, "Rowv")) {
if(nr != nc)
@@ -633,8 +637,8 @@
}
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)
+ min.raw <- min.breaks
+ max.raw <- max.breaks
}
z <- seq(min.raw, max.raw, length=length(col))
@@ -661,7 +665,7 @@
key.xlab <- "Value"
}
if (!is.na(key.xlab)) {
- mtext(side=1, key.xlab, line=par("mgp")[1], padj=0.5)
+ mtext(side=1, key.xlab, line=par("mgp")[1], padj=0.5, cex=par("cex") * par("cex.lab"))
}
if(density.info=="density")
@@ -687,7 +691,7 @@
if (is.null(key.ylab))
key.ylab <- "Density"
if (!is.na(key.ylab))
- mtext(side=2,key.ylab, line=par("mgp")[1], padj=0.5)
+ mtext(side=2,key.ylab, line=par("mgp")[1], padj=0.5, cex=par("cex") * par("cex.lab"))
}
else if(density.info=="histogram")
{
@@ -710,7 +714,7 @@
if (is.null(key.ylab))
key.ylab <- "Count"
if (!is.na(key.ylab))
- mtext(side=2,key.ylab, line=par("mgp")[1], padj=0.5)
+ mtext(side=2,key.ylab, line=par("mgp")[1], padj=0.5, cex=par("cex") * par("cex.lab"))
}
else
if (is.null(key.title))
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From: <wa...@us...> - 2015-05-01 15:28:36
|
Revision: 1995
http://sourceforge.net/p/r-gregmisc/code/1995
Author: warnes
Date: 2015-05-01 15:28:33 +0000 (Fri, 01 May 2015)
Log Message:
-----------
- heatmap.2: row traces could be plotted in the wrong order.
Modified Paths:
--------------
trunk/gplots/R/heatmap.2.R
Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R 2015-05-01 15:25:31 UTC (rev 1994)
+++ trunk/gplots/R/heatmap.2.R 2015-05-01 15:28:33 UTC (rev 1995)
@@ -554,7 +554,7 @@
{
retval$hline <- hline
hline.vals <- scale01(hline, min.scale, max.scale)
- for( i in rowInd )
+ for( i in 1:length(rowInd) )
{
if(!is.null(hline))
{
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