specifying hyperlinks on the plot
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@jane-fridlyand-106
Last seen 10.2 years ago
Hi, is there a capability in R/bioconductor for specifying hyperlinks from a , say, postscript or pdf plot. For instance, when I produce n by p image matrix with log2ratios and with all the clone names for the columns listed, is there a way to create a mark-up so that by clicking on a clone name to be taken to golden path (UCSC) info on the clone? If that is not possible, what would be the closest thing which is implemented? Thank you Jane ********************************************************************** **************** Jane Fridlyand, Postdoctoral Scientist UCSF Cancer Center, Box 0128 San Francisco, CA 94143-0128 Office: Room N412 Tel: (415)514-3302 Fax: (415)502-3179 ********************************************************************** ****************
Cancer Cancer • 1.7k views
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@vincent-j-carey-jr-4
Last seen 10 weeks ago
United States
> > Hi, > > is there a capability in R/bioconductor for specifying hyperlinks from a , > say, postscript or pdf plot. For instance, when I produce n by p image > matrix with log2ratios and with all the clone names for the columns > listed, is there a way to create a mark-up so that by clicking on a clone > name to be taken to golden path (UCSC) info on the clone? the short answer is no. a related question is why restrict to pdf or postscript? for x11 graphics, the locator function can be used to get information about mouse position. in my view the idea of specifying hyperlinks from a plot needs to be decomposed. problem 1 is getting useful info on mouse position. this requires some approximation because the user may not have good aim. problem 2 is translating info on mouse position to info about clone identity. problem 3 is getting from clone identity to golden path. problems 1 and 3 have solutions in R/bioconductor, and problem 2 does not seem so hard. but one could also entertain the idea of encoding hyperlink information in pdf with each spot. that idea is unattractive to me but it is closer to the intent of your question and i think it is possible. i would look at the hyperlink encoding capabilities of pdflatex for a start. to get started on the other approach, a function like function(apx=round) { apx(unlist(locator(1)),0); } will with the default setting of apx give you the integer coordinates closest to the mouse click on an R x11 device. if you have really good aim, set apx=function(x)x ... that setting of apx will also be useful if the coordinate processing is done under the hood. > > If that is not possible, what would be the closest thing which is > implemented? > > Thank you > > > Jane > > > > ******************************************************************** ****************** > Jane Fridlyand, Postdoctoral Scientist > UCSF Cancer Center, Box 0128 San Francisco, CA 94143-0128 > Office: Room N412 Tel: (415)514-3302 Fax: (415)502-3179 > ******************************************************************** ****************** > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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>>>>> "vincent" == Vincent Carey <525-2265 <stvjc@channing.harvard.edu>> writes: >> is there a capability in R/bioconductor for specifying hyperlinks from a , >> say, postscript or pdf plot. For instance, when I produce n by p image >> matrix with log2ratios and with all the clone names for the columns >> listed, is there a way to create a mark-up so that by clicking on a clone >> name to be taken to golden path (UCSC) info on the clone? vincent> the short answer is no. a related question is why restrict to pdf vincent> or postscript? for x11 graphics, the locator function can be used vincent> to get information about mouse position. Restriction may be the wrong word, but the general idea is solid, I think (i.e. mailing a hyperlinked PDF file to collaborators, for example). I think the general annotation problem (thinking along the lines of Vince) would be worth looking at. best, -tony -- A.J. Rossini Rsrch. Asst. Prof. of Biostatistics U. of Washington Biostatistics rossini@u.washington.edu FHCRC/SCHARP/HIV Vaccine Trials Net rossini@scharp.org -------------- http://software.biostat.washington.edu/ ---------------- FHCRC: M: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email UW: Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX (my tuesday/wednesday/friday locations are completely unpredictable.)
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On Saturday, November 2, 2002, at 01:55 PM, A.J. Rossini wrote: > > vincent> the short answer is no. a related question is why > restrict to pdf > vincent> or postscript? for x11 graphics, the locator function > can be used > vincent> to get information about mouse position. > > Restriction may be the wrong word, but the general idea is solid, I > think (i.e. mailing a hyperlinked PDF file to collaborators, for > example). > Even beyond this, PDF also supports embedded Javascript (for better or for worse) that could let you do potentially interesting things. Being able to generate active PDFs is definitely desirable (for posting or mailing to people who neither know nor care about R :-)). I don't see the current device driver model handling this very well. > I think the general annotation problem (thinking along the lines of > Vince) would be worth looking at. > > best, > -tony > > -- > A.J. Rossini Rsrch. Asst. Prof. of Biostatistics > U. of Washington Biostatistics rossini@u.washington.edu > FHCRC/SCHARP/HIV Vaccine Trials Net rossini@scharp.org > -------------- http://software.biostat.washington.edu/ ---------------- > FHCRC: M: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email > UW: Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX > (my tuesday/wednesday/friday locations are completely unpredictable.) > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > Byron Ellis (bellis@hsph.harvard.edu) "Oook" - The Librarian
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On Sat, 2 Nov 2002, Byron Ellis wrote: > > On Saturday, November 2, 2002, at 01:55 PM, A.J. Rossini wrote: > > > > > vincent> the short answer is no. a related question is why > > restrict to pdf > > vincent> or postscript? for x11 graphics, the locator function > > can be used > > vincent> to get information about mouse position. > > > > Restriction may be the wrong word, but the general idea is solid, I > > think (i.e. mailing a hyperlinked PDF file to collaborators, for > > example). > > > > Even beyond this, PDF also supports embedded Javascript (for better or > for worse) that could let you do potentially interesting things. Being > able to generate active PDFs is definitely desirable (for posting or > mailing to people who neither know nor care about R :-)). I don't see > the current device driver model handling this very well. ok, i am warming up to this idea, but i suspect that the density of hyperlinks to be handled by existing designs would be pretty light (at most a few links per line of narrative text or per embedded image). what jane is describing sounds very dense, and the quantity of metadata in a chip image could be substantial even if only one sort of link resolution were required ([x,y] to locuslink, e.g.). one would want to do the mapping from the geometry of the document (image) to the genomic annotation outside the document -- so i would assume that the document and a database would be involved at a minimum. i made a cursory search on active pdf and a check of the adobe site. i don't see anything immediately available for prototyping. one approach is to generate the pdf image in R and then apply some adobe tool to introduce a hyperlink. i would assume distiller could do this but i do not have access. if this worked we would then consider how best links could be introduced en masse.
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currently i am specifying clone names with a very small cex size and passing images on the biologists in the pdf format who then open it up in the Photoshop which i guess has a very good ability to zoom in (maybe adobe acrobat does too: i just don't have the full version). In any case focusing the mouse on the right clone names is not a problem for them. But i guess Vincent's concern is the file size with hyperlinks encoded for each clone name, is it right? Sparcing links across the genome would also be an option of course. What would be a reasonable number of hyperlinks per image? Jane ********************************************************************** **************** Jane Fridlyand, Postdoctoral Scientist UCSF Cancer Center, Box 0128 San Francisco, CA 94143-0128 Office: Room N412 Tel: (415)514-3302 Fax: (415)502-3179 ********************************************************************** **************** On Sun, 3 Nov 2002, Vincent Carey 525-2265 wrote: > > On Sat, 2 Nov 2002, Byron Ellis wrote: > > > > > On Saturday, November 2, 2002, at 01:55 PM, A.J. Rossini wrote: > > > > > > > > vincent> the short answer is no. a related question is why > > > restrict to pdf > > > vincent> or postscript? for x11 graphics, the locator function > > > can be used > > > vincent> to get information about mouse position. > > > > > > Restriction may be the wrong word, but the general idea is solid, I > > > think (i.e. mailing a hyperlinked PDF file to collaborators, for > > > example). > > > > > > > Even beyond this, PDF also supports embedded Javascript (for better or > > for worse) that could let you do potentially interesting things. Being > > able to generate active PDFs is definitely desirable (for posting or > > mailing to people who neither know nor care about R :-)). I don't see > > the current device driver model handling this very well. > > ok, i am warming up to this idea, but i suspect that the density > of hyperlinks to be handled by existing designs would be pretty > light (at most a few links per line of narrative text or per embedded image). > what jane is describing sounds very dense, and the quantity of > metadata in a chip image could be substantial even if only one > sort of link resolution were required ([x,y] to locuslink, e.g.). > one would want to do the mapping from the geometry of the document > (image) to the genomic annotation outside the document -- so i > would assume that the document and a database would be involved > at a minimum. > > i made a cursory search on active pdf and a check of the adobe > site. i don't see anything immediately available for prototyping. > one approach is to generate the pdf image in R and then apply > some adobe tool to introduce a hyperlink. i would assume distiller > could do this but i do not have access. if this worked we would > then consider how best links could be introduced en masse. > >
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>>>>> "jane" == Jane Fridlyand <janef@stat.berkeley.edu> writes: jane> currently i am specifying clone names with a very small cex size and jane> passing images on the biologists in the pdf format who then open it up in jane> the Photoshop which i guess has a very good ability to zoom in (maybe jane> adobe acrobat does too: i just don't have the full version). In any case jane> focusing the mouse on the right clone names is not a problem for them. But jane> i guess Vincent's concern is the file size with hyperlinks encoded for jane> each clone name, is it right? Sparcing links across the genome would also jane> be an option of course. What would be a reasonable number of hyperlinks jane> per image? Could you define "image" a bit better? I'm a bit confused (maybe others are, as well) if you mean "picture of a chip", or just "stuff in a PDF file"? If you are planning on clicking on a "spot", yikes, but just annotating text via hyperlinks, as long as its readable, should be fine... (well, readable and "mouse-able"). best, -tony -- A.J. Rossini Rsrch. Asst. Prof. of Biostatistics U. of Washington Biostatistics rossini@u.washington.edu FHCRC/SCHARP/HIV Vaccine Trials Net rossini@scharp.org -------------- http://software.biostat.washington.edu/ ---------------- FHCRC: M: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email UW: Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX (my tuesday/wednesday/friday locations are completely unpredictable.)
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Sorry!: i mean "image= stuff in pdf file": i.e. clicking on the hyperlinked text jane ********************************************************************** **************** Jane Fridlyand, Postdoctoral Scientist UCSF Cancer Center, Box 0128 San Francisco, CA 94143-0128 Office: Room N412 Tel: (415)514-3302 Fax: (415)502-3179 ********************************************************************** **************** On 3 Nov 2002, A.J. Rossini wrote: > >>>>> "jane" == Jane Fridlyand <janef@stat.berkeley.edu> writes: > > jane> currently i am specifying clone names with a very small cex size and > jane> passing images on the biologists in the pdf format who then open it up in > jane> the Photoshop which i guess has a very good ability to zoom in (maybe > jane> adobe acrobat does too: i just don't have the full version). In any case > jane> focusing the mouse on the right clone names is not a problem for them. But > jane> i guess Vincent's concern is the file size with hyperlinks encoded for > jane> each clone name, is it right? Sparcing links across the genome would also > jane> be an option of course. What would be a reasonable number of hyperlinks > jane> per image? > > Could you define "image" a bit better? I'm a bit confused (maybe > others are, as well) if you mean "picture of a chip", or just "stuff > in a PDF file"? > > If you are planning on clicking on a "spot", yikes, but just > annotating text via hyperlinks, as long as its readable, should be > fine... (well, readable and "mouse-able"). > > best, > -tony > > -- > A.J. Rossini Rsrch. Asst. Prof. of Biostatistics > U. of Washington Biostatistics rossini@u.washington.edu > FHCRC/SCHARP/HIV Vaccine Trials Net rossini@scharp.org > -------------- http://software.biostat.washington.edu/ ---------------- > FHCRC: M: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email > UW: Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX > (my tuesday/wednesday/friday locations are completely unpredictable.) > > > >
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BTW it would probably be sensible to cast this problem for r-devel, as it is a good problem of general annotation of statistical visualizations. On Sat, 2 Nov 2002, Byron Ellis wrote: > > On Saturday, November 2, 2002, at 01:55 PM, A.J. Rossini wrote: > > > > > vincent> the short answer is no. a related question is why > > restrict to pdf > > vincent> or postscript? for x11 graphics, the locator function > > can be used > > vincent> to get information about mouse position. > > > > Restriction may be the wrong word, but the general idea is solid, I > > think (i.e. mailing a hyperlinked PDF file to collaborators, for > > example). > > > > Even beyond this, PDF also supports embedded Javascript (for better or > for worse) that could let you do potentially interesting things. Being > able to generate active PDFs is definitely desirable (for posting or > mailing to people who neither know nor care about R :-)). I don't see > the current device driver model handling this very well. > > > I think the general annotation problem (thinking along the lines of > > Vince) would be worth looking at. > > > > best, > > -tony > > > > -- > > A.J. Rossini Rsrch. Asst. Prof. of Biostatistics > > U. of Washington Biostatistics rossini@u.washington.edu > > FHCRC/SCHARP/HIV Vaccine Trials Net rossini@scharp.org > > -------------- http://software.biostat.washington.edu/ ---------------- > > FHCRC: M: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email > > UW: Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX > > (my tuesday/wednesday/friday locations are completely unpredictable.) > > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > Byron Ellis (bellis@hsph.harvard.edu) > "Oook" - The Librarian > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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