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How to save pathway images with omics data overlaid?

asked 2016-09-01 11:28:24 -0600

IainB gravatar image


I am using the desktop version of pathway tools, currently version 19.0 on windows 7 professional. I have to use the desktop version as the PGDB I want to view is not available online.

I can make some nice images with omics data overlaid onto individual pathways. I first display the omics data on the cellular omics viewer, then right click on a pathway of interest, select pathway and then display pathway information in popup window.

I have two questions: -I am not able to save these images to a file, is there a way to do this? -More usefully I would like to be able to automatically gather all relevant pathways with omics data overlaid and have these saved to a file. Is there a way to do this, possibly using an API for example?

My key problem is saving many pathway images with data from multiple experiments (e.g multiple transcriptomic experiments) from an offline PGDB. Any other solutions on how to approach this would be greatly appreciated.

Best, Iain

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answered 2016-09-09 11:41:52 -0600

Suzanne Paley gravatar image

updated 2016-09-09 11:47:26 -0600

You can also use the Pathway Collage facility (which works on both desktop and web versions) to save a pathway image with omics data (either for a single pathway or for multiple pathways together) to a jpeg file. However, this only works interactively -- there is no API for it. Also, I don't think this facilty was available yet in v.19.0 -- I strongly recommend you upgrade to v.20.0 (not just for this functionality, either -- there have been other improvements to our handling of omics data, which may or may not be relevant to you).

There is actually no way to do what you want to automatically generate images for multiple pathways and multiple experiments using the desktop software.

As stated above, you may be able to do it by running your own web server, using web services to generate the pages (see, and then collecting up the generated temporary image files from the /tmp directory on your server (though they will have uninformative filenames), but even that will only work if your omics data has just a single timepoint (multi-timepoint data is rendered using flash popups, which aren't part of the generated image).

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answered 2016-09-01 13:11:24 -0600

ptools-admin gravatar image

Although you're using Pathway Tools in desktop mode, you can also run your version of Pathway Tools in "web mode". Have you tried doing that? Most images in desktop mode are not in a form that can be saved. However, you can save the images generated in web mode. Here's a brief summary of the differences in desktop vs web mode:

Please refer to Chapter 10 about web mode of the UserGuide under the Help menu of the desktop mode.

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Asked: 2016-09-01 11:28:24 -0600

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Last updated: Sep 09 '16