ISAHTML {eisa} | R Documentation

## 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.

### 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`.

### Value

These functions do not return a value. (They return `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.

### 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)

[Package eisa version 1.32.0 Index]