Re: [R] adding hyperlinked text to pdf plot
Hi Justin,
It sounds like you might be able to use the 'hyperplot()' function (in
the 'caroline' package) for creating an html imagemap around your
figure. This is assuming all that you want to do is interactivate a
2-dimensional scatter plot. You'd also lose PDF-pagination but the
auto-tabbing of most browsers from each independent hyperplot() call
should help you stay organized.
Say you use hyperplot() like so:
library(caroline)
chr1 <- data.frame(pos=1:1000, cov=rnorm(1000,10,1),
url=paste('http://my.genome.org/id=',1:1000,sep=''))
hyperplot(x='pos',y='cov', annout=chr1, link='url',
xlab='position', ylab='coverage')
chr2 <- data.frame(pos=1:1000, cov=rnorm(1000,10,1),
url=paste('http://my.genome.org/id=',1:1000,sep=''))
hyperplot(x='pos',y='cov', annout=chr2, link='url',
xlab='position', ylab='coverage')
#chr3 <-
#...etc...
With this approach you'd have each chromosome on a different tab.
Cheers,
Dave
On 12/5/2011 12:20 PM, Yihui Xie wrote:
Sorry I experimented with tikzDevice using \href{}{} but failed.
You can probably try the old image hotspot technique in HTML. I
remember someone did this before in R, but I cannot find the link to
the work now. The key is your need to use the two functions grconvertX
and grconvertY.
Regards,
Yihui
--
Yihui Xie
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA
On Mon, Dec 5, 2011 at 2:10 PM, Justin Fincher wrote:
For example, say I am plotting some data that is genomic and therefore
maps to a specific locus on the human genome, like a gene. I was
hoping to have the title of the plot display the gene name, but have
it be a link so that clicking on it would take you to those
coordinates on a public browser, like USCS's genome browser. So
basically, I was hoping to have text in a plot generated by R function
as a normal html-style link.
- Fincher
On Mon, Dec 5, 2011 at 14:09, Yihui Xie wrote:
It seems I missed the context of this post -- who is "you", and what
is "something other than the URL"?
I feel the tikzDevice package should be an option for the task.
Regards,
Yihui
--
Yihui Xie
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA
On Mon, Dec 5, 2011 at 12:39 PM, Justin Fincher wrote:
Howdy,
I have read that if you put a URL in the text of a plot being saved
into pdf, the result is a functional hyperlink. I am interested in
having text in a plot that is linked to a URL, but I would like the
text to be something other than the URL. Is this possible? Thank you.
- Fincher
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Re: [R] adding hyperlinked text to pdf plot
Hi On 6/12/2011 9:10 a.m., Justin Fincher wrote: For example, say I am plotting some data that is genomic and therefore maps to a specific locus on the human genome, like a gene. I was hoping to have the title of the plot display the gene name, but have it be a link so that clicking on it would take you to those coordinates on a public browser, like USCS's genome browser. So basically, I was hoping to have text in a plot generated by R function as a normal html-style link. The 'gridSVG' package will let you associate a hyperlink with text (or anything else) and produce SVG that can then be viewed in a web page (as long as your plot is a 'lattice' or 'ggplot2' one). Paul - Fincher On Mon, Dec 5, 2011 at 14:09, Yihui Xie wrote: It seems I missed the context of this post -- who is "you", and what is "something other than the URL"? I feel the tikzDevice package should be an option for the task. Regards, Yihui -- Yihui Xie Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Mon, Dec 5, 2011 at 12:39 PM, Justin Fincher wrote: Howdy, I have read that if you put a URL in the text of a plot being saved into pdf, the result is a functional hyperlink. I am interested in having text in a plot that is linked to a URL, but I would like the text to be something other than the URL. Is this possible? Thank you. - Fincher __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 p...@stat.auckland.ac.nz http://www.stat.auckland.ac.nz/~paul/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] adding hyperlinked text to pdf plot
Sorry I experimented with tikzDevice using \href{}{} but failed.
You can probably try the old image hotspot technique in HTML. I
remember someone did this before in R, but I cannot find the link to
the work now. The key is your need to use the two functions grconvertX
and grconvertY.
Regards,
Yihui
--
Yihui Xie
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA
On Mon, Dec 5, 2011 at 2:10 PM, Justin Fincher wrote:
> For example, say I am plotting some data that is genomic and therefore
> maps to a specific locus on the human genome, like a gene. I was
> hoping to have the title of the plot display the gene name, but have
> it be a link so that clicking on it would take you to those
> coordinates on a public browser, like USCS's genome browser. So
> basically, I was hoping to have text in a plot generated by R function
> as a normal html-style link.
>
> - Fincher
>
>
> On Mon, Dec 5, 2011 at 14:09, Yihui Xie wrote:
>> It seems I missed the context of this post -- who is "you", and what
>> is "something other than the URL"?
>>
>> I feel the tikzDevice package should be an option for the task.
>>
>> Regards,
>> Yihui
>> --
>> Yihui Xie
>> Phone: 515-294-2465 Web: http://yihui.name
>> Department of Statistics, Iowa State University
>> 2215 Snedecor Hall, Ames, IA
>>
>>
>>
>> On Mon, Dec 5, 2011 at 12:39 PM, Justin Fincher wrote:
>>> Howdy,
>>> I have read that if you put a URL in the text of a plot being saved
>>> into pdf, the result is a functional hyperlink. I am interested in
>>> having text in a plot that is linked to a URL, but I would like the
>>> text to be something other than the URL. Is this possible? Thank you.
>>>
>>> - Fincher
>>>
>>> __
>>> R-help@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>
>> --
>> This message has been scanned for viruses and
>> dangerous content by MailScanner, and is
>> believed to be clean.
>>
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] adding hyperlinked text to pdf plot
On 05/12/2011 3:10 PM, Justin Fincher wrote:
For example, say I am plotting some data that is genomic and therefore
maps to a specific locus on the human genome, like a gene. I was
hoping to have the title of the plot display the gene name, but have
it be a link so that clicking on it would take you to those
coordinates on a public browser, like USCS's genome browser. So
basically, I was hoping to have text in a plot generated by R function
as a normal html-style link.
Just use Sweave, and put the URL in a LaTeX \href{URL}{text} tag, not in
the R code. This can be generated in R code in
\Sexp{}. It's not part of the PDF image, but it's part of the final
document.
Duncan Murdoch
- Fincher
On Mon, Dec 5, 2011 at 14:09, Yihui Xie wrote:
> It seems I missed the context of this post -- who is "you", and what
> is "something other than the URL"?
>
> I feel the tikzDevice package should be an option for the task.
>
> Regards,
> Yihui
> --
> Yihui Xie
> Phone: 515-294-2465 Web: http://yihui.name
> Department of Statistics, Iowa State University
> 2215 Snedecor Hall, Ames, IA
>
>
>
> On Mon, Dec 5, 2011 at 12:39 PM, Justin Fincher wrote:
>> Howdy,
>> I have read that if you put a URL in the text of a plot being saved
>> into pdf, the result is a functional hyperlink. I am interested in
>> having text in a plot that is linked to a URL, but I would like the
>> text to be something other than the URL. Is this possible? Thank you.
>>
>> - Fincher
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] adding hyperlinked text to pdf plot
For example, say I am plotting some data that is genomic and therefore maps to a specific locus on the human genome, like a gene. I was hoping to have the title of the plot display the gene name, but have it be a link so that clicking on it would take you to those coordinates on a public browser, like USCS's genome browser. So basically, I was hoping to have text in a plot generated by R function as a normal html-style link. - Fincher On Mon, Dec 5, 2011 at 14:09, Yihui Xie wrote: > It seems I missed the context of this post -- who is "you", and what > is "something other than the URL"? > > I feel the tikzDevice package should be an option for the task. > > Regards, > Yihui > -- > Yihui Xie > Phone: 515-294-2465 Web: http://yihui.name > Department of Statistics, Iowa State University > 2215 Snedecor Hall, Ames, IA > > > > On Mon, Dec 5, 2011 at 12:39 PM, Justin Fincher wrote: >> Howdy, >> I have read that if you put a URL in the text of a plot being saved >> into pdf, the result is a functional hyperlink. I am interested in >> having text in a plot that is linked to a URL, but I would like the >> text to be something other than the URL. Is this possible? Thank you. >> >> - Fincher >> >> __ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] adding hyperlinked text to pdf plot
It seems I missed the context of this post -- who is "you", and what is "something other than the URL"? I feel the tikzDevice package should be an option for the task. Regards, Yihui -- Yihui Xie Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Mon, Dec 5, 2011 at 12:39 PM, Justin Fincher wrote: > Howdy, > I have read that if you put a URL in the text of a plot being saved > into pdf, the result is a functional hyperlink. I am interested in > having text in a plot that is linked to a URL, but I would like the > text to be something other than the URL. Is this possible? Thank you. > > - Fincher > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] adding hyperlinked text to pdf plot
On Dec 5, 2011, at 1:39 PM, Justin Fincher wrote:
Howdy,
I have read that if you put a URL in the text of a plot being saved
into pdf, the result is a functional hyperlink.
Don't believe everything you read.
pdf("test.pdf")
plot(1,1,main="http://test.gov/some.htm";)
dev.off()
"Non-functioning" text.
I am interested in
having text in a plot that is linked to a URL, but I would like the
text to be something other than the URL. Is this possible? Thank you.
- Fincher
David Winsemius, MD
West Hartford, CT
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Re: [R] adding hyperlinked text to pdf plot
On 05-Dec-11 18:39:21, Justin Fincher wrote: > Howdy, >I have read that if you put a URL in the text of a plot > being saved into pdf, the result is a functional hyperlink. > I am interested in having text in a plot that is linked to > a URL, but I would like the text to be something other than > the URL. Is this possible? Thank you. > > - Fincher The "kosher" method of doing this kind of thing (and a host of other interactive elements in a PDF file) would be to incorporate a so-called PDFmark into the PDF code. See for instance: http://www.pdflib.com/developer/technical-documentation/ books/pdfmark-primer/ There are various ways of doing this in some document-preparation programs, but I don't know whether it would be easy to do this when creating a PDF in R. In mt experience, this involves first passing via PostScript. Any comments, anyone? Ted. E-Mail: (Ted Harding) Fax-to-email: +44 (0)870 094 0861 Date: 05-Dec-11 Time: 18:58:53 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] adding hyperlinked text to pdf plot
Howdy, I have read that if you put a URL in the text of a plot being saved into pdf, the result is a functional hyperlink. I am interested in having text in a plot that is linked to a URL, but I would like the text to be something other than the URL. Is this possible? Thank you. - Fincher __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
