annHeatmap: Annotated heatmaps
Description
Creating heatmaps with annotated columns
Usage
annHeatmap(x, ...)
"annHeatmap"(x, annotation, dendrogram = list(clustfun = hclust, distfun = dist, Col = list(status = "yes"), Row = list(status = "hidden")), cluster = NULL, labels = NULL, legend = TRUE, ...)
"annHeatmap"(x, ...)
Arguments
x
either a numerical matrix with the data for the central heatmap (for the default method) or an object of class ExpressionSet
annotation
a data frame containing the annotation for the columns of x
dendrogram
a list controlling the options for row- and column dendrogram, see annHeatmap2
cluster
a list controlling the options for clustering rows and columns of x
, see annHeatmap2
labels
a list controlling the row- and column labels as well as their location and size, see annHeatmap2
legend
either a logical value, indicating whether to draw a legend at the default location determined by the function, or one of the sides of the plot (1-4), see annHeatmap2
...
extra options passed to annHeatmap2
Value
An object of class annHeatmap
Warning
These are currently simple convenience functions that allow quick plotting, but little control over the finer details. This may change in the future, but for now, if you want to do anything fancy, you should invoke annHeatmap2
directly.Details
These functions generate an object representing the heatmap; in order to produce graphical output, you have to invoke the plot
method, see Examples.
Examples
Run this code
## Default method
set.seed(219)
mat = matrix(rnorm(100), ncol=5)
ann = data.frame(Class=c("A","A","B","A","B"))
map1 = annHeatmap(mat, ann)
plot(map1)
## Expression set
require(Biobase)
data(sample.ExpressionSet)
map2 = annHeatmap(sample.ExpressionSet)
plot(map2)
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