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segmentPlot {ADaCGH}

Segment plots for aCGH
Package: 
ADaCGH
Version: 
1.5-3

Description

A (more or less) uniform interface and uniform output to segment plots for the available aCGH methods in this package. By the default, it produces html files (and associated png) with an image map with links to additional information. You need Python for all this to work.

Usage

segmentPlot(x, geneNames, yminmax, 
            idtype = "ug", organism = "Hs",
            arrays = NULL, chroms = NULL,
            colors = c("orange", "red", "green", "blue", "black"),
            html_js = FALSE,
            superimp = FALSE,
            imgheight = 500,
            genomewide_plot = FALSE,
            ...)

Arguments

x
The fitted object of the appropriate class.
geneNames
A vector of gene names.
yminmax
A vector of the form (min, max) for the minimum and maximum used in the figures.
idtype
The type of id of the gene name; one of ('None', 'cnio', 'affy', 'clone', 'acc', 'ensembl', 'entrez', 'ug') corresponding, respectively to None, CNIO ID, Affymetrix, Clone ID, Accession Number, Ensembl ID, Entrez ID, UniGene.
organism
The organism; one of ('None', 'Hs', 'Mm', 'Rn') corresponding, respectively, to None, Homo sapiens, Mus musculus (mouse) and Rattus norvegicus (rat).
arrays
The arrays to plot (a vector with the numbers, the indices, of the arrays), or NULL for plotting all arrays.
chroms
The chromosomes to plot (a vector with the numbers, the indices, of the chromsomes), or NULL for plotting all chromosomes.
colors
Colors used for plotting: a five element vector denoting colors for non-altered points, gained, lost, the smoothed line and the horizontal line at 0.
html_js
Produce the html figures including lots of Javascript? Default is FALSE.
superimp
Produce the figures that superimpose all arrays into a single plot? Default is FALSE. Superimposed plots will soon NOT be available!
imgheight
The image height when generating png. Default is 500.
genomewide_plot
Do a genomewide plot. Default is FALSE. Genomewide plots will soon NOT be available.
...
Other arguments, passed to the underlying plotting functions.

Values

Used only for its side effects of producing plots. Beware that you will get from a few to a lot of HTML and png files written to your local file system.

References

Diaz-Uriarte, R. and Rueda, O.M. (2006). ADaCGH: an R package and web-based application for the analysis of aCGH data. Tech. report. http://www.ligarto.org/rdiaz/Papers/adacgh.pdf, http://adacgh.bioinfo.cnio.es.

Note

Most of the arguments are not really needed in most cases. See examples below.

You NEED a working Python for this function to work and produce the imagemaps.

See Also

pSegmentWavelets, pSegmentACE, pSegmentDNAcopy, pSegmentPSW,

Examples

## See examples under \link{pSegmentDNAcopy}

Author(s)

Ramon Diaz-Uriarte rdiaz02@gmail.com

Documentation reproduced from package ADaCGH, version 1.5-3. License: GPL (>= 3)