problem with "save image"

[Daniel Bauer]

I am trying to create a figure from some tracks I have loaded into my IGV session. I go to "Save image" and choose File Format "*.svg". When I go to open the file in Illustrator, it shows a Progress bar with PNG, then gives error "Clipping will be lost on roundtrip to Tiny, The following items could not be imported properly". When it finally opens it doesn't look like the tracks but rather blocks of gray where the tracks and labels should be. I have tried both IGV2.1 and 2.2, have installed Java7, and am using Mac OS X 10.7.5. Previously I was able to create svg image files from IGV without problem.

[Jacob Silterra]

In brief you have a few options. 

 (1) The black and gray rectangles you see can be removed in illustrator, they are in layers over the actual figure. Ungroup everything and delete those rectangles, you should see normal images underneath

(2)  The "batch" screenshot option does not suffer from this, you can write a small batch script to get the screenshot then run it from the file menu. See http://www.broadinstitute.org/igv/PortCommands. The behavior here is somewhat different, the screenshot will include much more in the way of imagery.

(3) I've opened these files with Inkscape and they look fine without adjustment.

On Mon, Feb 18, 2013 at 10:41 AM, Daniel Bauer <daniele...@gmail.com> wrote:

I am trying to create a figure from some tracks I have loaded into my IGV session. I go to "Save image" and choose File Format "*.svg". When I go to open the file in Illustrator, it shows a Progress bar with PNG, then gives error "Clipping will be lost on roundtrip to Tiny, The following items could not be imported properly". When it finally opens it doesn't look like the tracks but rather blocks of gray where the tracks and labels should be. I have tried both IGV2.1 and 2.2, have installed Java7, and am using Mac OS X 10.7.5. Previously I was able to create svg image files from IGV without problem.

--
 
---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

--
Jacob Silterra
Software Engineer
Broad Institute

[Jim Robinson]

A few more details,

This appears to be a problem on Macs with Java 7,  I haven't observed it on other platform + java combinations but if anyone else has please post here.   We are working on a better solution for the next release, but for the time being please try one of the workarounds Jacob outlines and let us know if you need further assistance.

Jim