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Last data update: 2014.03.03

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

overview

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`.
`...`	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

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(made4)
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
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/made4/overview.Rd_%03d_medium.png", width=480, height=480)
> ### Name: overview
> ### Title: Draw boxplot, histogram and hierarchical tree of gene expression
> ###   data
> ### Aliases: overview
> ### Keywords: hplot manip
> 
> ### ** Examples
> 
>   data(khan)
> 
>   logkhan<-log2(khan$train)
>   print(class(logkhan))
[1] "data.frame"
>   overview(logkhan, title="Subset of Khan Train")
>   overview(logkhan, classvec=khan$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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>