[BioC] xtable links

[James W. MacDonald]

Hi Tim,

Tim Smith 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)

Your html is malformed:

 > mat2
      [,1] [,2] [,3] [,4]
[1,] "1"  "7"  "13" "<a href=\"http:\\www.nytimes.com\">19</a>"
[2,] "2"  "8"  "14" "<a href=\"http:\\www.nytimes.com\">20</a>"
[3,] "3"  "9"  "15" "<a href=\"http:\\www.nytimes.com\">21</a>"
[4,] "4"  "10" "16" "<a href=\"http:\\www.nytimes.com\">22</a>"
[5,] "5"  "11" "17" "<a href=\"http:\\www.nytimes.com\">23</a>"
[6,] "6"  "12" "18" "<a href=\"http:\\www.nytimes.com\">24</a>"

So you need to fix that first (e.g.,
"<A href="http:\\www.nytimes.com\">19</A>")

In addition, you don't use write.table() with xtable. You want to use

print(mx, file="test.html", type="html")

Also you might want to add caption.placement="top" if you want the 
caption to be at the top of the page.

Best,

Jim



> 
> write.table(tt2,'test.html',quote=F)
> 
> 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]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662