sam2html {siggenes}R Documentation

HTML page for a SAM object

Description

Generates a html page for a SAM object. This html page can contain general information as the number of differentially expressed genes and the estimated FDR, the SAM plot and gene-specific information on the differentially expressed genes.

Usage

 sam2html(sam.out, delta, filename, addStats = TRUE, addPlot = TRUE, addGenes = TRUE,
        ll = FALSE, refseq = TRUE, symbol = TRUE, omim = TRUE, ug = TRUE,
        chipname = "", cdfname = NULL, n.digits = 3, bg.col = "white", text.col = "black",
        link.col = "blue", plotArgs = plotArguments(), bg.plot.adjust = FALSE, 
        plotname = NULL, plotborder = 0, tableborder = 1, new.window = TRUE, ...)

Arguments

sam.out a SAM object
delta a numerical value specifying the Delta value
filename character string naming the file in which the output should be stored. Must have the suffix ".html"
addStats logical indicating if general information as the number of differentially expressed genes and the estimated FDR should be added to the html page
addPlot logical indicating if the SAM plot should be added to the html page
addGenes logical indicating if gene-specific information on the differentially expressed genes should be added to the html page
ll logical indicating if Locus Links should be added to the output. Ignored if addGenes=FALSE
refseq logical indicating if RefSeq links should be added to the output. Ignored if addGenes=FALSE
symbol logical indicating if the gene symbols should be added to the output. Ignored if addGenes=FALSE
omim logical indicating if OMIM links should be added to the output. Ignored if addGenes=FALSE
ug logical indicating if UniGene links should be added to the output. Ignored if addGenes=FALSE
chipname character string specifying the chip type used in the analysis. Must be specified as in the meta-data section of Bioconductor (e.g., "hgu133a" for the Affymetrix HG-U133A chip). Need not to be specified if cdfname is specified. Ignored if addGenes=FALSE
cdfname character string specifying the cdf name of the used chip. Must exactly follow the nomenclatur of the Affymetrix chips (e.g., "HG-U133A" for the Affymetrix HG-U133A chip). If specified, links to the Affymetrix webpage for the interesting genes will be added to the output. Ignored if addGenes=FALSE
n.digits integer specifying the number of decimal places used in the output
bg.col specification of the background color of the html page. See ?par for how colors can be specified
text.col specification of the color of the text used in the html page. See ?par for how colors can be specified
link.col specification of the color of the links used in the html file. See ?par for how colors can be specified
plotArgs further arguments for generating the SAM plot. These are the arguments used by sam.plot2 and plot, respectively. See ?plotArgs for these arguments. Ignored if addPlot=FALSE
bg.plot.adjust logical indicating if the background color of the SAM plot should be the same as the background color of the html page. If FALSE (default) the background of the plot is white. Ignored if addPlot=FALSE
plotname character string naming the file in which the SAM plot is stored. This file is needed when the SAM plot should be added to the html page. If not specified the SAM plot will be stored as png file in the same folder as the html page. Ignored if addPlot=FALSE
plotborder integer specifying the thickness of the border around the plot. By default, plotborder=0, i.e. no border is drawn around the plot. Ignored if addPlot=FALSE
tableborder integer specifying the thickness of the border of the table. Ignored if addGenes=FALSE
new.window logical indicating if the links should be opened in a new window
... further graphical arguments for the SAM plot. See ?plot.default and ?par. Ignored if addPlot=FALSE

Author(s)

Holger Schwender, holger.schw@gmx.de

See Also

SAM-class, sam, link.genes, link.siggenes, sam2excel, plotArguments


[Package siggenes version 1.4.0 Index]