heatmap {aCGH}  R Documentation 
Clusters samples and produces heatmapp of the observed log2ratios.
heatmap(x, imp = TRUE, Rowv = NA, Colv = NULL, distfun = dist, hclustfun = hclust, add.expr, symm = FALSE, revC = identical(Colv, "Rowv"), scale = "none", na.rm = TRUE, margins = c(5, 5), ColSideColors, RowSideColors, cexRow = 0.2 + 1 / log10(nr), cexCol = 0.2 + 1 / log10(nc), labRow = NULL, labCol = NULL, main = NULL, xlab = NULL, ylab = NULL, verbose = getOption("verbose"), methodR = "ward", methodC = "ward", zlm = c(0.5, 0.5), ...)
x 
object of the aCGH object 
imp 
logical variable indicating whether
log2.ratios.imputed or log2.ratios slot of
aCGH should be used. Defaults to imputed value (TRUE).

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' 
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.

distfun 
function used to compute the distance (dissimilarity) between both rows and columns. Defaults to 'dist'. 
hclustfun 
function used to compute the hierarchical clustering when 'Rowv' or 'Colv' are not dendrograms. Defaults to 'hclust' 
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. 
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. 
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; 
verbose 
logical indicating if information should be printed. 
methodR 
method to use for clustering rows. defaults to "ward" 
methodC 
method to use for clustering columns. defaults to "ward" 
zlm 
all the values greater or equal than zlm are set to zlm  0.01. a;; value less or equal to zlm are set to zlm + 0.01 
... 
additional arguments passed on to 'image', e.g., 'col' specifying the colors. 
This function is almost identical to the heatmap
in base
R. The slight modifications are that (1) a user can specify clustering
method for rows and columns; (2) all the values outside specified
limits are floored to be 0.01 less than a limit; (3) default values
are different. Note that using default option of imp
(TRUE)
produces nicer looking plots as all missing values are removed.
Invisibly, a list with components
crowInd 
row index permutation vector as returned by
order.dendrogram

colInd 
row index permutation vector as returned by
order.dendrogram

heatmap function in base R
#default plotting method for the aCGH object data(colorectal) plot(colorectal) #to produce smoother looking heatmap, use imp = T: this will use imputed #slot of aCGH object plot(colorectal, imp = TRUE)