heatmap3
From heatmap3 v1.1.1
by Shilin Zhao
heatmap3
The function heatmap3 is completely compatible with the original R function heatmap, and provides more new features.
Usage
heatmap3(x, Rowv = NULL, Colv = if (symm) "Rowv" else NULL, distfun = function(x) as.dist(1  cor(t(x), use = "pa")), balanceColor = F, ColSideLabs, RowSideLabs, showColDendro = T, showRowDendro = T, col = colorRampPalette(c("navy", "white", "firebrick3"))(1024), legendfun, method = "complete", ColAxisColors = 0, RowAxisColors = 0, hclustfun = hclust, reorderfun = function(d, w) reorder(d, w), add.expr, symm = FALSE, revC = identical(Colv, "Rowv"), scale = c("row", "column", "none"), na.rm = TRUE, ColSideFun, ColSideAnn, ColSideWidth = 0.4, ColSideCut, colorCell, highlightCell, file = "heatmap3.pdf", topN = NA, filterFun = sd, margins = c(5, 5), ColSideColors, RowSideColors, cexRow = 0.2 + 1/log10(nrow(x)), cexCol = 0.2 + 1/log10(ncol(x)), lasRow = 2, lasCol = 2, labRow = NULL, labCol = NULL, main = NULL, xlab = NULL, ylab = NULL, keep.dendro = FALSE, verbose = getOption("verbose"), useRaster = if (ncol(x) * nrow(x) >= 50000) TRUE else FALSE, ...)
Arguments
 x
 numeric matrix of the values to be plotted.
 Rowv
 determines if and how the row dendrogram should be
computed and reordered. Either a
dendrogram
or a vector of values used to reorder the row dendrogram orNA
to suppress any row dendrogram (and reordering) or by default,NULL
, see ‘Details’ below.  Colv
 determines if and how the column dendrogram should be
reordered. Has the same options as the
Rowv
argument above and additionally whenx
is a square matrix,Colv = "Rowv"
means that columns should be treated identically to the rows (and so if there is to be no row dendrogram there will not be a column one either).  distfun
 function used to compute the distance (dissimilarity)
between both rows and columns. Defaults to
dist
.  balanceColor
 logical indicating if the colors need to be balanced so that the median color will represent the 0 value. The default value is F.
 ColSideLabs
 label for ColSideColors
 RowSideLabs
 label for RowSideColors
 showColDendro
 logical indicating if the coloum dendrogram should be plotted (when Colv isn't NA).
 showRowDendro
 logical indicating if the row dendrogram should be plotted (when Rowv isn't NA).
 col
 specifying the colors, used in
image
function.  legendfun
 function used to generate legend in top left of the figure. If not specified, the color bar will be plotted. The users can use any plot functions to generate their own legend. Or a function
showLegend
is also provided as a example.  method
 the agglomeration method to be used by
hclust
function. This should be (an unambiguous abbreviation of) one of "ward", "single", "complete", "average", "mcquitty", "median" or "centroid".  ColAxisColors
 integer indicating which coloum of ColSideColors will be used as colors for labels in coloum axis. The default value is 0, which means all coloum labels will be in black color.
 RowAxisColors
 integer indicating which coloum of RowSideColors will be used as colors for labels in row axis. The default value is 0, which means all row labels will be in black color.
 hclustfun
 function used to compute the hierarchical clustering
when
Rowv
orColv
are not dendrograms. Defaults tohclust
. Should take as argument a result ofdistfun
and return an object to whichas.dendrogram
can be applied.  reorderfun
function(d, w)
of dendrogram and weights for reordering the row and column dendrograms. The default usesreorder.dendrogram
. add.expr
 expression that will be evaluated after the call to
image
. Can be used to add components to the plot.  symm
 logical indicating if
x
should be treated symmetrically; can only be true whenx
is a square matrix.  revC
 logical indicating if the column order should be
rev
ersed for plotting, such that e.g., for the symmetric case, the symmetry axis is as usual.  scale
 character indicating if the values should be centered and
scaled in either the row direction or the column direction, or
none. The default is
"row"
ifsymm
false, and"none"
otherwise.  na.rm
 logical indicating whether
NA
's should be removed.  ColSideFun
 function used to generate annotation and labeling figure in column side. The users can use any plot functions to generate their own figure. And a function
showAnn
is also provided as a example.  ColSideAnn
 data frame with continuous and factor variables as annotation information. This parameter will be sorted by coloum dendrogram and then passed to ColSideFun.
 ColSideWidth
 numeric the height of column side area, which can be used by ColSideFun function.
 ColSideCut
 numeric the value to be used in cutting coloum dendrogram. The dendrogram and annotation will be divided into different parts and labeled respectively.
 colorCell
 A data.frame with 3 columns, indicating which cells will be colored by specific colors. The first column is row index, second column is column index, and the third column is color.
 highlightCell
 A data.frame with 3 or 4 columns, indicating which cells will be highlighted by rectangles with specific colors. The first column is row index, second column is column index, the third column is color for rectangle border, and the optional forth column is width for rectangle border.
 file
 pdf file name, only works when topN was used.
 topN
 vector a list of numbers. topN genes will be used to generate the heatmaps.
 filterFun
 function used to filter genes, such as sd, mean, sum. It will be used in a apply function to caculate for each row.
 margins
 numeric vector of length 2 containing the margins
(see
par(mar = *)
) for column and row names, respectively.  ColSideColors
 (optional) character vector of length
ncol(x)
containing the color names for a horizontal side bar that may be used to annotate the columns ofx
.  RowSideColors
 (optional) character vector of length
nrow(x)
containing the color names for a vertical side bar that may be used to annotate the rows ofx
.  cexRow,cexCol
 positive numbers, used as cex.axis in for the row or column axis labeling. The defaults currently only use number of rows or columns, respectively.
 lasRow,lasCol
 the style of row or column axis labels.
 labRow,labCol
 character vectors with row and column labels to use; these default to rownames(x) or colnames(x), respectively.
 main,xlab,ylab
 main, x and yaxis titles; defaults to none.
 keep.dendro
 logical indicating if the dendrogram(s) should be
kept as part of the result (when
Rowv
and/orColv
are not NA).  verbose
 logical indicating if information should be printed.
 useRaster
 logical; if TRUE a bitmap raster is used to plot the image instead of polygons. The grid must be regular in that case, otherwise an error is raised.
 ...
 additional arguments passed on to
image
.
Value

The same return value as
hclust
function.
Examples
#gererate data
set.seed(123456789)
rnormData<matrix(rnorm(1000), 40, 25)
rnormData[1:15, seq(6, 25, 2)] = rnormData[1:15, seq(6, 25, 2)] + 2
rnormData[16:40, seq(7, 25, 2)] = rnormData[16:40, seq(7, 25, 2)] + 4
colnames(rnormData)<c(paste("Control", 1:5, sep = ""), paste(c("TrtA", "TrtB"),
rep(1:10,each=2), sep = ""))
rownames(rnormData)<paste("Probe", 1:40, sep = "")
ColSideColors<cbind(Group1=c(rep("steelblue2",5), rep(c("brown1", "mediumpurple2"),10)),
Group2=sample(c("steelblue2","brown1", "mediumpurple2"),25,replace=TRUE))
colorCell<data.frame(row=c(1,3,5),col=c(2,4,6),color=c("green4","black","orange2"),
stringsAsFactors=FALSE)
highlightCell<data.frame(row=c(2,4,6),col=c(1,3,5),color=c("black","green4","orange2"),
lwd=1:3,stringsAsFactors=FALSE)
#A simple example
heatmap3(rnormData,ColSideColors=ColSideColors,showRowDendro=FALSE,colorCell=colorCell,
highlightCell=highlightCell)
#A more detail example
ColSideAnn<data.frame(Information=rnorm(25),Group=c(rep("Control",5), rep(c("TrtA", "TrtB"),10)))
row.names(ColSideAnn)<colnames(rnormData)
RowSideColors<colorRampPalette(c("chartreuse4", "white", "firebrick"))(40)
result<heatmap3(rnormData,ColSideCut=1.2,ColSideAnn=ColSideAnn,ColSideFun=function(x)
showAnn(x),ColSideWidth=0.8,RowSideColors=RowSideColors,col=colorRampPalette(c("green",
"black", "red"))(1024),RowAxisColors=1,legendfun=function() showLegend(legend=c("Low",
"High"),col=c("chartreuse4","firebrick")),verbose=TRUE)
#annotations distribution in different clusters and the result of statistic tests
result$cutTable
Community examples
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