[BioC] xtable links

[Sean Davis]

On Fri, Dec 5, 2008 at 4:08 PM, Tim Smith <tim_smith_666 at yahoo.com> wrote:
> Hi,
>
> I was trying to get hyperlinks using xtable, but couldn't get the hyperlinks to function properly. For example, if I use
>
> ## Try to link NY times website to every figure in column 4
> mat <- matrix(1:43,6,5)
> mat[,5] <- "http://nytimes.com"
>
> for(i in 1:nrow(mat)){
>    strr <-  paste('<a href="', mat[i,5],'">', mat[i,4], '</a>', sep='')
>    mat[i,4] <- strr
> }
> mat2 <- mat[,1:4]
>
> caption = 'test'
> mx <- xtable(mat2,caption=caption)
> tt = print(mx, type="html",include.rownames=F)
> tt1 <- gsub('lt /a','lt/a',tt,fixed=T)
> tt2 <- gsub('lt a','lta',tt1,fixed=T)
>
> write.table(tt2,'test.html',quote=F)

xtable converts the table to HTML.  You won't want to use write.table
on that.  Use something like writeLines().  Also, the HTML output by
xtable is only the "table" part; you will need to put appropriate HTML
header, body, etc. around the table in order for it to work in a
browser.

> However, if I open 'test.html' in IE, the hyperlinks don't seem to work. What am I doing wrong?
>
> thanks.
>
>
>
>        [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>