makeOldHTMLReport: Creating and initializing an HTMLReport object

Description

This is the function one shoud use to instantiate an HTMLReport. It basically creates the report in the appropriate place, creating directories if needed. Special care should be taken if non-default javacsript or css files are used, as detailed below.

Usage

makeOldHTMLReport(shortName, title = NULL, reportDirectory = ".",
baseUrl = "localhost", basePath = NULL, page = NULL, link.css = NULL,
link.javascript = NULL, overwrite.js=TRUE)

Arguments

shortName

A short name for the report. It is used as the base of the HTML file.

title

The title for the page. It will be used in the title element in the page head, and will also be written at the top of the page.

reportDirectory

A character string giving the directory where the report will be written.

baseUrl

A character string giving the location of the page in terms of HTML locations.

basePath

A character string giving the location of the page in terms of filesystem locations.

page

The file handle for the html page, returned from the hwriter function openPage.

link.css

A character vector of file URLs detailing where to get style sheets. If unset, the default styling for ReportingTools is used.

link.javascript

A character vector of file URLs detailing where to get javascript. If unset, the default javascript libraries for ReportingTools are used.

overwrite.js

logical whether css and javascript files should be overwritten when copied into the report directory.

Value

An HTMLReport object with an open file handle to an HTML page.

Details

Care should be used if link.javascript or link.css are set. If the javascript libraries for ReportingTools aren't linked, then it is likely that the resulting pages will not be as interactive as the default. The default css files are found in the extdata/csslib directory of the ReportingTools package, while the default javascript libraries are found in the extdata/jslib directory of the ReportingTools package. Both css and js files are copied from the package extdata directory into the reportDirectory of the HTMLReport.

Examples

Run this code

my.df <- data.frame(EGID = c("103", "104", "105", "106", "107"),
                    RPKM = c(4, 5, 3, 100, 75),
                    DE = c("Yes", "Yes", "No", "No", "No"))
html.report <- makeOldHTMLReport(shortName = "my_html_file",
    reportDirectory = "reportDirectory")
publish(my.df, html.report)