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Last data update: 2014.03.03

R: Expression matrix plots for ISA modules

expPlot

R Documentation

Expression matrix plots for ISA modules

Description

These functions create an expression matrix plot for an ISA module. The gene and sample scores are also plotted.

Usage

expPlotCreate (eset, modules, which, norm = c("sample", "raw", "feature"))
expPlot (epo, scores = TRUE)                                              
expPlotColbar (epo)

Arguments

`eset`	An `ExpressionSet` or `ISAExpressionSet` object. If an `ExpressionSet` object is supplied (and the `norm` argument is not set to ‘raw’), then it is normalised by calling `ISANormalize` on it. A subset of `eset` is selected that corresponds to the features included in `modules`.
`norm`	Character constant, specifies whether and how to normalize the expression values to plot. ‘raw’ plots the raw expression values, ‘feature’ the expression values scaled and centered for each feature (=gene) separately and if ‘sample’ is specified then the expression values are centered and scaled separately for each sample.
`modules`	An `ISAModules` object.
`which`	Numeric scalar, which module to plot.
`scores`	Logical scalar, whether to plot the scores as well.
`epo`	An object returned by `expPlotCreate`.

Details

expPlotCreate creates an object that contains all data for performing the image plot and returns it. The reason for not plotting it directly is, that the size of the plot is usually different in different cases, and the opening of the graphics device is delayed until expPlotCreate returns.

In the returned object, the weight and height entries give the optimal size of the image, in pixels.

expPlot creates the expression plot.

expPlotColbar plots a color bar for the expression plot.

Value

expPlotCreate returns an ISAexpPlot object. It is a named list and has several entries, the important ones:

`width`	Numeric scalar, the optimal width of the plot.
`height`	Numeric scalar, the optimal height of the plot.

expPlot returns, invisibly, a named list with members:

`coords`	A list with two entries: `x` and `y`, both numeric vectors of length two. They give the position of the actual expression matrix on the plot.
`gene.width`	Numeric scalar, the width of one box on the image plot, in pixels; if the image size is exactly the suggested one.
`cond.height`	Numeric scalar, the height of one box on the image plot, in pixels; if the image size is exactly the suggested one.

expPlotColbar returns NULL, invisibly.

Author(s)

Gabor Csardi csardi.gabor@gmail.com

References

Bergmann S, Ihmels J, Barkai N: Iterative signature algorithm for the analysis of large-scale gene expression data Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Mar;67(3 Pt 1):031902. Epub 2003 Mar 11.

Examples

data(ALLModulesSmall)
library(ALL)
data(ALL)

ep <- expPlotCreate(ALL, ALLModulesSmall, 1)
ep

if (interactive()) {
  expPlot(ep)
}

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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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(eisa)
Loading required package: isa2
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/eisa/exp.plot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: expPlot
> ### Title: Expression matrix plots for ISA modules
> ### Aliases: expPlot expPlotCreate expPlotColbar print.ISAexpPlot
> ### Keywords: cluster
> 
> ### ** Examples
> 
> data(ALLModulesSmall)
> library(ALL)
> data(ALL)
> 
> ep <- expPlotCreate(ALL, ALLModulesSmall, 1)
> ep
An expression plot for an ISA module, use 'expPlot' to plot it.
> 
> #if (interactive()) {
>   expPlot(ep)
> #}
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>