Plotting tools - best output format? PDF, PNG, ...
Hi all, I'm working on a simple plotting tool, and currently I am using PDF output since this is vector based (so it can be rescaled without loss of quality) and can be edited easily enough for use in publications. However, at least on my OS/Browser, Galaxy does not show the PDF files in situ, the "eye" button acts like a download link. Is this a bug? If I switch to making a PNG file, then clicking on the "eye" button shows the image directly in the center panel (nice), but PNG is not a great format for detailed figures or printing. Looking over the tools which come with Galaxy under tools/plotting/*.xml all use PDF or PNG. How about SVG? Don't most of the mainline browsers have reasonably good SVG support built in (possibly via a plugin)? Peter
On Wed, Apr 20, 2011 at 10:07 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi all,
I'm working on a simple plotting tool, and currently I am using PDF output since this is vector based (so it can be rescaled without loss of quality) and can be edited easily enough for use in publications.
However, at least on my OS/Browser, Galaxy does not show the PDF files in situ, the "eye" button acts like a download link. Is this a bug?
Looks like a Firefox issue/setting - false alarm: On our local Galaxy, with a PDF entry in the history, and as a control http://nar.oxfordjournals.org/content/39/7/2492.full.pdf+html which should show a PDF embedded on the left: Windows XP, Internet Explorer 7.05730.13 - NAR shows PDF on left, good - Clicking on the eye, shows the PDF in the central panel, good. - Clicking on the disk, saves the PDF, good. Windows XP, Chrome 10.0.648.204 - NAR shows PDF on left, good - Clicking on the eye, shows the PDF in the central panel, good. - Clicking on the disk, saves the PDF, good. Windows XP, Firefox 3.6.13 - NAR shows PDF on left, good - Clicking on the eye, shows the PDF in the central panel, good. - Clicking on the disk, saves the PDF, good. Linux CentOS, Firefox 3.6.13 - NAR downloads PDF, shows left pane empty, usable. - Clicking on the eye, downloads the PDF, usable. - Clicking on the disk, saves the PDF, good. Mac OS X 10.6, Firefox 4.0 - NAR downloads PDF, shows left pane empty, usable. - Clicking on the eye, downloads the PDF, usable. - Clicking on the disk, saves the PDF, good. Mac OS X 10.6, Safari 5.0.5 - NAR shows PDF on left, good - Clicking on the eye, shows the PDF in the central panel, good. - Clicking on the disk, saves the PDF, good. So it looks like Firefox can (probably dependent on the user's settings) download PDF files rather than show them in situ. That's fine, and not specific to Galaxy. Peter
Hi Peter, On Apr 20, 2011, at 11:07 AM, Peter Cock wrote:
Hi all,
...<cut>...
How about SVG? Don't most of the mainline browsers have reasonably good SVG support built in (possibly via a plugin)?
Yep, SVG support is pretty good nowadays especially in FireFox and Opera. Safari, IE and Chrome have only partial support, but for simple charts without 3D filters it works fine. I've added SVG as a datatype to my Galaxy and this works great. You won't need a plugin; in fact the old Adobe SVG plugin is depreciated already for a few years now and no longer compatible with recent browser versions. The nice benefit of SVG in addition to not needing a plugin is that the image can scale with the surrounding text if you zoom in your browser (without loosing resolution). The disadvantage is that although my users know what a PDF file is and can process them for posters/manuscripts, most of them never heard of SVG and get stuck when it doesn't import into PowerPoint et al. :( Cheers, Pi
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On Wed, Apr 20, 2011 at 4:30 PM, Pieter Neerincx <pieter.neerincx@gmail.com> wrote:
Hi Peter,
On Apr 20, 2011, at 11:07 AM, Peter Cock wrote:
Hi all,
...<cut>...
How about SVG? Don't most of the mainline browsers have reasonably good SVG support built in (possibly via a plugin)?
Yep, SVG support is pretty good nowadays especially in FireFox and Opera. Safari, IE and Chrome have only partial support, but for simple charts without 3D filters it works fine. I've added SVG as a datatype to my Galaxy and this works great. You won't need a plugin; in fact the old Adobe SVG plugin is depreciated already for a few years now and no longer compatible with recent browser versions.
I looked at SVG about a year ago, and was pretty impressed. I did run into some issues, particularly with links, and opted to use PNG files in the end. Since then we've finally dropped IE6, so hopefully SVG would be safe now. Are your changes to add SVG as a datatype to Galaxy public? I'd like to suggest that be merged to the trunk.
The nice benefit of SVG in addition to not needing a plugin is that the image can scale with the surrounding text if you zoom in your browser (without loosing resolution).
The disadvantage is that although my users know what a PDF file is and can process them for posters/manuscripts, most of them never heard of SVG and get stuck when it doesn't import into PowerPoint et al. :(
Do they cope with PDF? Peter
participants (2)
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Peter Cock -
Pieter Neerincx