ISA.html: Create HTML summary pages from the result of modular analysis
In eisa: Expression data analysis via the Iterative Signature Algorithm

Description Usage Arguments Details Value Author(s) References See Also Examples

These functions create various sophisticated HTML pages from a set of ISA biclusters.

ISAHTMLTable (modules, target.dir, which = NULL,
    template = system.file("autogen", package = "eisa"), GO = NULL, 
    KEGG = NULL, miRNA = NULL, CHR = NULL, htmltitle = NULL, 
    notes = NULL, seed = NULL, extra = list()) 

ISAHTMLModules (eset, modules, which = NULL, target.dir, 
    template = system.file("autogen", package = "eisa"), GO = NULL,    
    KEGG = NULL, miRNA = NULL, CHR = NULL, cond.to.include = NULL,     
    cond.col = "white", sep = NULL, seed = NULL, condPlot = TRUE)

ISAHTML (eset, modules, target.dir, template = system.file("autogen", 
    package = "eisa"), GO, KEGG, miRNA = NULL, CHR = NULL, htmltitle = NULL, 
    notes = NULL, seed = NULL, table.extra = list(), cond.to.include = NULL, 
    cond.col = "white", sep = NULL, condPlot = TRUE, which = NULL)

`modules`	An `ISAModules` object.
`target.dir`	Character vector of length one, the directory in which the result is placed. It is created if it does not exist.
`which`	Numeric vector, which modules to include in the table (`ISAHTMLTable`); or, which modules to create HTML pages for (`ISAHTML` and `ISAHTMLModules`). All modules are used if this argument is `NULL`, which is the default.
`template`	The directory containing the HTML template files. By default the template included in the `eisa` package is used.
`GO`	List of three `GOListHyperGResult` objects, as returned by the `ISAGO` function.
`KEGG`	A `KEGGListHyperGResult` object, usually the output of the `ISAKEGG` function.
`miRNA`	A `miRNAListHyperGResult` object, or `NULL`. See also the `ISAmiRNA` function.
`CHR`	A `CHRListHyperGResult` object or `NULL`, see also the `ISACHR` function.
`htmltitle`	Character vector of length one, the title of the HTML page.
`notes`	Character vector of length one. Optional HTML text, on the default template it is placed on the top of the page, above the table.
`seed`	Either `NULL`, or a character vector, with an optional column that is added to the module table.
`extra`	Extra columns to put in the HTML table. It should be a named list of character vectors, each with the same length as the number of modules.
`table.extra`	This is passed to `ISAHTMLTable` as the `extra` argument.
`eset`	An `ExpressionSet` or `ISAExpressionSet` object. If an `ExpressionSet` object is supplied, then it is normalised by calling `ISANormalize` on it.
`cond.to.include`	Numeric or character vector, specifies which columns of the phyenotype data of the original expression matrix are included in the tables of samples. By default the first six columns are included.
`cond.col`	This is passed to `condPlot` as the `col` argument.
`sep`	This is passed to `condPlot` as the `sep` argument.
`condPlot`	Logical scalar, whether to create condition plots. If an alternative biclustering method was used to find the modules, then probably it makes no sense creating condition plots for them.

ISAHTMLTable creates an HTML page, a summary of the results of the modular analysis, including enrichment analysis of the modules.

ISAHTMLModules creates a separate HTML page for each module, including the following elements:

An expression plot of the genes and samples in the module, including the ISA scores. This is done by calling expPlot.
Gene Ontology tree plots for the enriched GO terms, separately for the three ontologies. These are produced by calling gograph.
Tables for the enriched Gene Ontology terms, separately for the three ontologies.
A table for the enriched KEGG pathways.
A table for the enriched miRNA families.
The list of genes in the module.
The list of samples in the module.
A condition plot (if the condPlot argument is TRUE), see condPlot.

By default, clicking on the rows of the table generated by ISAHTMLTable is linked to the HTML page of the module, generated by ISAHTMLModules.

ISAHTML calls both ISAHTMLTable and ISAHTMLModules.

These functions do not return a value. (They return NULL, invisibly.)

Gabor Csardi csardi.gabor@gmail.com

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.

The vignette included in the eisa package.

## Not run: 
# Load data
library(ALL)
data(ALL)
data(ALLModulesSmall)

# Calculate enrichment
GO <- ISAGO(ALLModulesSmall)
KEGG <- ISAKEGG(ALLModulesSmall)
CHR <- ISACHR(ALLModulesSmall)

# Generate HTML summary
htmldir <- tempdir()
ISAHTML(ALL, modules=ALLModulesSmall, target.dir=htmldir,
        GO=GO, KEGG=KEGG, CHR=CHR)

# Open a browser to view the summary
if (interactive()) {
  browseURL(URLencode(paste("file://", htmldir, "/maintable.html", sep="")))
}

## End(Not run)