ISAHTML(eisa)
ISAHTML()所属R语言包：eisa
Create HTML summary pages from the result of modular analysis
创建模块化分析的结果HTML摘要页
译者：生物统计家园网 机器人LoveR
描述----------Description----------
These functions create various sophisticated HTML pages from a set of ISA biclusters.
这些功能创建一套的ISA biclusters各种复杂的HTML页面。
用法----------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)
参数----------Arguments----------
参数：modules
An ISAModules object.
ISAModules对象。
参数：target.dir
Character vector of length one, the directory in which the result is placed. It is created if it does not exist.
字符长度为1的向量，结果被放置的目录中。创建它，如果它不存在。
参数：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.
数字向量，模块包括在表（ISAHTMLTable），或者，该模块创建HTML页面（ISAHTML和ISAHTMLModules）。如果这种说法是的NULL，这是默认的，所有的模块都使用。
参数：template
The directory containing the HTML template files. By default the template included in the eisa package is used.
包含HTML模板文件的目录。默认情况下使用eisa包中包含的模板。
参数：GO
List of three GOListHyperGResult objects, as returned by the ISAGO function.
3GOListHyperGResultISAGO函数返回的对象名单。
参数：KEGG
A KEGGListHyperGResult object, usually the output of the ISAKEGG function.
一个KEGGListHyperGResult对象，通常是ISAKEGG函数的输出。
参数：miRNA
A miRNAListHyperGResult object, or NULL. See also the ISAmiRNA function.
一个miRNAListHyperGResult对象，或NULL。参见ISAmiRNA功能。
参数：CHR
A CHRListHyperGResult object or NULL, see also the ISACHR function.
一个CHRListHyperGResult对象或NULL，看到ISACHR功能。
参数：htmltitle
Character vector of length one, the title of the HTML page.
特征向量的长度为一，HTML页面的标题。
参数：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.
特征向量的长度为一。可选的HTML文本，它的默认模板放置在页面的顶部，上面的表。
参数：seed
Either NULL, or a character vector, with an optional column that is added to the module table.
要么NULL，或特征向量，一个可选的列被添加到模块表。
参数：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.
额外的列放在HTML表。它应该是一个性格的向量，每个模块数量相同长度的命名列表。
参数：table.extra
This is passed to ISAHTMLTable as the extra argument.
这是传递给ISAHTMLTableextra参数。
参数：eset
An ExpressionSet or ISAExpressionSet object. If an ExpressionSet object is supplied, then it is normalised by calling ISANormalize on it.
ExpressionSet或ISAExpressionSet对象。如果ExpressionSet对象提供的，那么它被调用ISANormalize标准化。
参数：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.
数字或字符向量，指定原始表达式矩阵phyenotype数据列包括样品表。默认情况下，上半年列。
参数：cond.col
This is passed to condPlot as the col argument.
这是传递给condPlotcol参数。
参数：sep
This is passed to condPlot as the sep argument.
这是传递给condPlotsep参数。
参数：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.
逻辑标量，是否要创造条件的图。如果另一种双聚类方法被用来查找模块，那么很可能它是没有意义的，为他们创造条件的图。
Details
详情----------Details----------
ISAHTMLTable creates an HTML page, a summary of the results of the modular analysis, including enrichment analysis of the modules.
ISAHTMLTable创建一个HTML页面，模块化分析，包括模块富集分析结果的摘要。
ISAHTMLModules creates a separate HTML page for each module, including the following elements:
ISAHTMLModules为每个模块创建一个单独的HTML页面，包括下列因素：
An expression plot of the genes and samples in the module, including the ISA scores. This is done by calling expPlot.
表达的基因和样品中的模块，包括ISA分数图。这是通过调用expPlot。
Gene Ontology tree plots for the enriched GO terms, separately for the three ontologies. These are produced by calling gograph.
基因本体富集的GO术语，分别为三个本体树的图。这些是由调用gograph。
Tables for the enriched Gene Ontology terms, separately for the three ontologies.
表富集基因本体论方面，三个本体分开。
A table for the enriched KEGG pathways.
丰富KEGG通路表。
A table for the enriched miRNA families.
丰富的miRNA家族表。
The list of genes in the module.
在模块列表中的基因。
The list of samples in the module.
在模块列表中的样本。
A condition plot (if the condPlot argument is TRUE), see condPlot.
一个条件图（如果condPlot参数是TRUE），看到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.
默认情况下，点击对ISAHTMLTable生成的表中的行链接的HTML页面模块，生成ISAHTMLModules。
ISAHTML calls both ISAHTMLTable and ISAHTMLModules.
ISAHTML呼吁双方ISAHTMLTable和ISAHTMLModules。
值----------Value----------
These functions do not return a value. (They return NULL, invisibly.)
这些函数不返回值。 （它们返回NULL，看不见的。）
作者（S）----------Author(s)----------
Gabor Csardi <a href="mailto:Gabor.Csardi@unil.ch">Gabor.Csardi@unil.ch</a>
参考文献----------References----------
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.
参见----------See Also----------
The vignette included in the eisa package.
eisa包中包含的小品文。
举例----------Examples----------
# Load data[加载数据]
library(ALL)
data(ALL)
data(ALLModulesSmall)
# Calculate enrichment[计算富集]
GO <- ISAGO(ALLModulesSmall)
KEGG <- ISAKEGG(ALLModulesSmall)
CHR <- ISACHR(ALLModulesSmall)
# Generate HTML summary[生成的HTML摘要]
htmldir <- tempdir()
ISAHTML(ALL, modules=ALLModulesSmall, target.dir=htmldir,
GO=GO, KEGG=KEGG, CHR=CHR)
# Open a browser to view the summary[打开一个浏览器来查看摘要]
if (interactive()) {
browseURL(URLencode(paste("file://", htmldir, "/maintable.html", sep="")))
}
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
|
发表于 2012-2-25 17:13:57
