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 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. |
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)