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Last data update: 2014.03.03

R: Display gene list as a HTML page

htmlPage

R Documentation

Display gene list as a HTML page

Description

Given a set of index to a data.frame containing gene names information. We create a web page with one element per genes that contains URLs links to various external database links. E.g Operon oligodatabase , Riken, GenBank and PubMed web sites.

Usage

htmlPage(genelist, filename = "GeneList.html", geneNames =
                 Gnames, mapURL = SFGL, othernames, title, table.head,
                 table.center = TRUE, disp = c("browser", "file")[1])

table2html(restable, filename = "GeneList.html", mapURL = SFGL,
                 title, table.head, table.center = TRUE, disp =
                 c("browser", "file")[1])

Arguments

`restable`	A data.frame that contains only the information you wish to display in the html file. The rows corresponds to a different DNA spots.
`genelist`	A numeric vector of index to a data.frame
`filename`	The name of the file to store the HTML in.
`geneNames`	A data.frame containing the information related the each DNA spots.
`mapURL`	A matrix of characters containing the URL for various external database. E.g `SFGL`.
`othernames`	A data.frame containing other information.
`title`	Title of the HTML page
`table.head`	A character vector of column labels for the table
`table.center`	A logical indicating whether the table should be centered
`disp`	Either "File" or "Browser" (default is Browser). File will save the information in html file, while Browser will create an html files and display information in the user's browser.

Details

This function is an extension to ll.htmlpage

Value

No value is return, the function produce a html file "filename" and output the results in a browser.

Author(s)

Yee Hwa Yang

Examples

##library(annotate)
data(swirl)
Gnames <- maGeneTable(swirl)
swirlmap <- mapGeneInfo(Name = "none", ID="genbank")
## htmlPage(100:110, geneNames = Gnames, mapURL = swirlmap, title="Swirl")

moreinfo <- round(maM(swirl), 2)
swirlmap <- mapGeneInfo(Name = "pubmed", ID="genbank")
##htmlPage(100:110, geneNames = Gnames, mapURL = swirlmap, othernames=moreinfo, title="Swirl", disp="file")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(marray)
Loading required package: limma
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/marray/htmlPage.Rd_%03d_medium.png", width=480, height=480)
> ### Name: htmlPage
> ### Title: Display gene list as a HTML page
> ### Aliases: htmlPage table2html
> ### Keywords: file
> 
> ### ** Examples
> 
> ##library(annotate)
> data(swirl)
> Gnames <- maGeneTable(swirl)
> swirlmap <- mapGeneInfo(Name = "none", ID="genbank")
> ## htmlPage(100:110, geneNames = Gnames, mapURL = swirlmap, title="Swirl")
> 
> moreinfo <- round(maM(swirl), 2)
> swirlmap <- mapGeneInfo(Name = "pubmed", ID="genbank")
> ##htmlPage(100:110, geneNames = Gnames, mapURL = swirlmap, othernames=moreinfo, title="Swirl", disp="file")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>