| Line 16... |
Line 16... |
| 16 |
restrictions imposed by the dendrogram is carried out.
|
16 |
restrictions imposed by the dendrogram is carried out.
|
| 17 |
}
|
17 |
}
|
| 18 |
\usage{
|
18 |
\usage{
|
| 19 |
heatmap(x, Rowv = NULL, Colv = if(symm)"Rowv" else NULL,
|
19 |
heatmap(x, Rowv = NULL, Colv = if(symm)"Rowv" else NULL,
|
| 20 |
distfun = dist, hclustfun = hclust,
|
20 |
distfun = dist, hclustfun = hclust,
|
| 21 |
reorderfun = function(d,w) reorder(d,w),
|
21 |
reorderfun = function(d, w) reorder(d, w),
|
| 22 |
add.expr, symm = FALSE, revC = identical(Colv, "Rowv"),
|
22 |
add.expr, symm = FALSE, revC = identical(Colv, "Rowv"),
|
| 23 |
scale = c("row", "column", "none"), na.rm = TRUE,
|
23 |
scale = c("row", "column", "none"), na.rm = TRUE,
|
| 24 |
margins = c(5, 5), ColSideColors, RowSideColors,
|
24 |
margins = c(5, 5), ColSideColors, RowSideColors,
|
| 25 |
cexRow = 0.2 + 1/log10(nr), cexCol = 0.2 + 1/log10(nc),
|
25 |
cexRow = 0.2 + 1/log10(nr), cexCol = 0.2 + 1/log10(nc),
|
| 26 |
labRow = NULL, labCol = NULL, main = NULL,
|
26 |
labRow = NULL, labCol = NULL, main = NULL,
|
| Line 44... |
Line 44... |
| 44 |
between both rows and columns. Defaults to \code{\link{dist}}.}
|
44 |
between both rows and columns. Defaults to \code{\link{dist}}.}
|
| 45 |
\item{hclustfun}{function used to compute the hierarchical clustering
|
45 |
\item{hclustfun}{function used to compute the hierarchical clustering
|
| 46 |
when \code{Rowv} or \code{Colv} are not dendrograms. Defaults to
|
46 |
when \code{Rowv} or \code{Colv} are not dendrograms. Defaults to
|
| 47 |
\code{\link{hclust}}. Should take as argument a result of \code{distfun}
|
47 |
\code{\link{hclust}}. Should take as argument a result of \code{distfun}
|
| 48 |
and return an object to which \code{\link{as.dendrogram}} can be applied.}
|
48 |
and return an object to which \code{\link{as.dendrogram}} can be applied.}
|
| 49 |
\item{reorderfun}{function(d,w) of dendrogram and weights for
|
49 |
\item{reorderfun}{\code{function(d, w)} of dendrogram and weights for
|
| 50 |
reordering the row and column dendrograms. The default uses
|
50 |
reordering the row and column dendrograms. The default uses
|
| 51 |
\code{\link{reorder.dendrogram}}.}
|
51 |
\code{\link{reorder.dendrogram}}.}
|
| 52 |
\item{add.expr}{expression that will be evaluated after the call to
|
52 |
\item{add.expr}{expression that will be evaluated after the call to
|
| 53 |
\code{image}. Can be used to add components to the plot.}
|
53 |
\code{image}. Can be used to add components to the plot.}
|
| 54 |
\item{symm}{logical indicating if \code{x} should be treated
|
54 |
\item{symm}{logical indicating if \code{x} should be treated
|
| Line 151... |
Line 151... |
| 151 |
main = "heatmap(<Mtcars data>, ..., scale = \"column\")")
|
151 |
main = "heatmap(<Mtcars data>, ..., scale = \"column\")")
|
| 152 |
\testonly{
|
152 |
\testonly{
|
| 153 |
## no row dendrogram (nor reordering) at all:
|
153 |
## no row dendrogram (nor reordering) at all:
|
| 154 |
heatmap(x, Rowv = NA, col = cm.colors(256), scale = "column",
|
154 |
heatmap(x, Rowv = NA, col = cm.colors(256), scale = "column",
|
| 155 |
ColSideColors = cc, margins = c(5,10),
|
155 |
ColSideColors = cc, margins = c(5,10),
|
| 156 |
xlab = "xlab", ylab = "ylab")# no main
|
156 |
xlab = "xlab", ylab = "ylab") # no main
|
| 157 |
}
|
157 |
}
|
| 158 |
## "no nothing"
|
158 |
## "no nothing"
|
| 159 |
heatmap(x, Rowv = NA, Colv = NA, scale = "column",
|
159 |
heatmap(x, Rowv = NA, Colv = NA, scale = "column",
|
| 160 |
main = "heatmap(*, NA, NA) ~= image(t(x))")
|
160 |
main = "heatmap(*, NA, NA) ~= image(t(x))")
|
| 161 |
%% also want example using the `add.exp' argument!
|
161 |
%% also want example using the `add.exp' argument!
|
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