ISAHTML {eisa} | R Documentation |
These functions create various sophisticated HTML pages from a set of ISA biclusters.
ISAHTMLTable (modules, target.dir, which = seq_len(length(modules)), template = system.file("autogen", package = "eisa"), GO = NULL, KEGG = NULL, miRNA = NULL, CHR = NULL, htmltitle = NULL, notes = NULL, seed = NULL) ISAHTMLModules (eset, modules, which = seq_len(length(modules)), 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, cond.to.include = NULL, cond.col = "white", sep = NULL, condPlot = TRUE)
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
(for ISAHTMLTable ); or, which modules to
create HTML pages for (ISAHTMLModules ). All modules are
used by 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 deafult template it is placed on the top of the page, above the table. |
seed |
Either NULL , or a character vector, with optional
column that is added to the module table. |
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:
expPlot
.
overlapPlot
gograph
.
condPlot
argument is
TRUE
), see condPlot
.
By default, clicking on the lines 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 Gabor.Csardi@unil.ch
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.
# 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=""))) }