ISAHTML package:eisa R Documentation
_C_r_e_a_t_e _H_T_M_L _s_u_m_m_a_r_y _p_a_g_e_s _f_r_o_m _t_h_e _r_e_s_u_l_t _o_f _m_o_d_u_l_a_r _a_n_a_l_y_s_i_s
_D_e_s_c_r_i_p_t_i_o_n:
These functions create various sophisticated HTML pages from a set
of ISA biclusters.
_U_s_a_g_e:
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)
_A_r_g_u_m_e_n_t_s:
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.
_D_e_t_a_i_l_s:
'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'.
* Overlap plot of all modules, see 'overlapPlot'
* 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 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'.
_V_a_l_u_e:
These functions do not return a value. (They return 'NULL',
invisibly.)
_A_u_t_h_o_r(_s):
Gabor Csardi Gabor.Csardi@unil.ch
_R_e_f_e_r_e_n_c_e_s:
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.
_S_e_e _A_l_s_o:
The vignette included in the 'eisa' package.
_E_x_a_m_p_l_e_s:
# 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="")))
}