overview {made4} | R Documentation

## Draw boxplot, histogram and hierarchical tree of gene expression data

### Description

Very simple wrapper function that draws a boxplot, histogram and hierarchical tree of expression data

### Usage

    overview(dataset, labels = NULL, title = "", classvec = NULL,
      hc = TRUE, boxplot = TRUE, hist = TRUE, returnTree=FALSE)

### Arguments

`dataset` | A `matrix`, `data.frame`, `ExpressionSet` or `marrayRaw-class`. If the input is gene expression data in a `matrix` or `data.frame`. The rows and columns are expected to contain the variables (genes) and cases (array samples) respectively.
`labels` | Vector, labels to be placed on samples in plots. Default is rownames(dataset).
`title` | Character, label to be placed on plots. Default is `NULL`.
`classvec` | A `factor` or `vector` which describes the classes in columns of the `dataset`. Default is `NULL`. If included columns (array samples) on the dendrogram will be coloured by class.
`hc` | Logical. Draw dendrogram of hierarchical cluster analysis of cases. Default is `TRUE`.
`boxplot` | Logical. Draw boxplot. Default is `TRUE`.
`hist` | Logical. Draw histogram. Default is `TRUE`.
`returnTree` | Logical. Return the hieracrhical cluster analysis results. Default is `FALSE`.

### Details

The hierarchical plot is produced using average linkage cluster analysis with Pearson's correlation metric as described by Eisen et al.,1999.

### Author(s)

Aedin Culhane

### See Also

See also as `boxplot`, `hclust`, `hist`

### Examples

      data(khan)

      logkhan<-log2(khan$train)
      print(class(logkhan))
      overview(logkhan, title="Subset of Khan Train")

      overview(logkhan, classvec=khan$train.classes,
      labels=khan$train.classes,title="Subset of Khan Train")

      overview(logkhan, classvec=khan$train.classes,
      labels=khan$train.classes,title="Subset of Khan Train", boxplot=FALSE,
      his=FALSE)

[Package made4 version 1.66.0 Index]