annotate (version 1.50.0)

htmlpage: Functions to build HTML pages

Description

This function is designed to create an HTML table containing both static information as well as links to various online annotation sources.

Usage

htmlpage(genelist, filename, title, othernames, table.head, table.center = TRUE, repository = list("en"), ...)

Arguments

genelist

A list or data.frame of character vectors containing ids to be made into hypertext links. See details for more information.

filename

A filename for the resultant HTML table.

title

A title for the table.

othernames

A list or data.frame of other things to add to the table. These will not be hyperlinks. The list of othernames can contain vectors, matrices, data.frames or lists.

table.head

A character vector of column headers for the table.

table.center

Center the table? Defaults to TRUE.

repository

A list of repositories to use for creating the hypertext links. Currently available repositories include 'gb' (GenBank), 'en' (EntrezGene), 'omim' (Online Mendelian Inheritance in Man), 'sp' (SwissProt), 'affy' (Affymetrix), 'ug' (UniGene), 'fb' (FlyBase), 'go' (Gene Ontology), 'ens' (Ensembl). Additional repositories can easily be added. See setRepository for more information.

...

Further arguments to be passed. See details for more information.

Value

This function is used only for the side effect of creating an HTML table.

Details

This function will accept a list or data.frame of character vectors, each containing different ids that are to be turned into hyperlinks (e.g., a list containing affy ids, genbank accession numbers, and Entrez Gene ids). For instances where there are more than one id per gene, use a sub-list of character vectors. See the vignette 'HowTo: Get HTML Output' for more information. Othernames should be a list or data.frame. Again, if there are multiple entries for a given gene, use a sub-list. This is more easily explained using an example - please see the examples section below and the above mentioned vignette.

In even the simplest case the genelist, othernames and repository have to be lists. A simple character vector will not suffice.

Note that this function now uses xtable to create the HTML table, and there is the ability to pass some arguments on to either xtable or print.xtable. One such argument would be 'append=TRUE', which would allow one to put lots of tables in one page, as long as the filename argument remained the same.

Additionally, the Ensembl repository needs a species argument in order to form a usable URI. This argument can be passed in the form of e.g., species = "Homo\_sapiens". Note the capitalization of the genus, and the separation by an underscore (\_).

Examples

  ## A very simple example. Two columns, one with links, the other without.

  gos <- paste("GO:000000", 1:9, sep="")
  notlinks <- LETTERS[1:9]

  htmlpage(list(gos), "simple.html", "Two column data", list(notlinks),
           c("GO IDs", "Letters"), repository = list("go"))

  if(!interactive())
    file.remove("simple.html")

  ## A more complex example with multiple links per cell
  ## first we create data to annotate
  unigene <- list("Hs.600536",c("Hs.596913","HS.655491"),"Hs.76704")
  refseq <- list(c("NM_001030050", "NM_001030047", "NM_001648",
  "NM_001030049"), "NM_000860", c("NM_001011645", "NM_000044"))
  entrez <- c("354", "3248", "367")
  genelist <- list(unigene, refseq, entrez)

  ## now some other data

  symb <- c("KLK3","HPGD","AR")
  desc <- c("Prostate-specific antigen precursor",
            "15-hydroxyprostaglandin dehydrogenase",
            "Androgen receptor")
  t.stat <- c(40.21, -22.14, 21.56)
  p.value <- rep(0,3)
  fold.change <- c(3.54, -2.35, 3.18)
  expression <- matrix(c(11.78, 11.69, 11.62, 8.17, 5.78, 5.58, 5.68,
                         8.26, 9.08, 9.28, 9.19, 6.05), ncol=4, byrow=TRUE)

  otherdata <- list(symb, desc, t.stat, p.value, fold.change, expression)
  table.head <- c("UniGene", "RefSeq", "EntrezGene", "Symbol",
                  "Description", "t-stat", "p-value", "fold change",
                  paste("Sample", 1:4))

  htmlpage(genelist, "test.html", "Some gene expression data", otherdata,
           table.head, repository = list("ug","gb","en"))

  if(!interactive())
    file.remove("test.html")