overview: Draw boxplot, histogram and hierarchical tree of gene...
In made4: Multivariate analysis of microarray data using ADE4

Description Usage Arguments Details Author(s) See Also Examples

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

1 2	overview(dataset, labels = NULL, title = "", classvec = NULL, hc = TRUE, boxplot = TRUE, hist = TRUE, returnTree=FALSE)

`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`.

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

Aedin Culhane

See also as boxplot, hclust, hist

  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)

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