The function heatmap3 is completely compatible with the original R function heatmap, and provides more new features.

```
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, ...)
```

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 or
`NA`

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* when `x`

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`

or `Colv`

are not dendrograms. Defaults to
`hclust`

. Should take as argument a result of `distfun`

and return an object to which `as.dendrogram`

can be applied.

reorderfun

`function(d, w)`

of dendrogram and weights for
reordering the row and column dendrograms. The default uses
`reorder.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
**symm**etrically; can only be true when `x`

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"`

if `symm`

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 of `x`

.

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 of `x`

.

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 y-axis titles; defaults to none.

keep.dendro

logical indicating if the dendrogram(s) should be
kept as part of the result (when `Rowv`

and/or `Colv`

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`

.

The same return value as `hclust`

function.

# NOT RUN { #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 # }