Usage
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), ...)
Arguments
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 y-axis 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.