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

In SamGG/made4: Multivariate analysis of microarray data using ADE4

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.
...	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

  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)

SamGG/made4 documentation built on Sept. 29, 2020, 1:33 p.m.