annHeatmap: Annotated heatmaps

In alexploner/Heatplus: Heatmaps with row and/or column covariates and colored clusters

Description

Creating heatmaps with annotated columns

Usage

annHeatmap(x, ...)

## Default S3 method:
annHeatmap(
  x,
  annotation,
  dendrogram = list(clustfun = hclust, distfun = dist, Col = list(status = "yes"), Row
    = list(status = "hidden")),
  cluster = NULL,
  labels = NULL,
  legend = TRUE,
  ...
)

## S3 method for class 'ExpressionSet'
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
...	extra options passed to annHeatmap2
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

Details

These functions generate an object representing the heatmap; in order to produce graphical output, you have to invoke the plot method, see Examples.

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.

See Also

annHeatmap2, plot.annHeatmap

Examples

    ## 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)

alexploner/Heatplus documentation built on May 23, 2021, 2:01 p.m.