eisa (version 1.24.0)

ISAHTML: Create HTML summary pages from the result of modular analysis

Description

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

Usage

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)

Arguments

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.

Value

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

Details

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.

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.

See Also

The vignette included in the eisa package.

Examples

## 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)