overview: Draw boxplot, histogram and hierarchical tree of gene...

Description Usage Arguments Details Author(s) See Also Examples

View source: R/overview.R

Description

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

Usage

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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.

...

further arguments passed to or from other methods.

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

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  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)

Example output

Loading required package: ade4
Loading required package: RColorBrewer
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: scatterplot3d
[1] "data.frame"

made4 documentation built on Nov. 1, 2018, 3:44 a.m.