Creating Standardized images of networks

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William Love

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Jan 27, 2016, 11:34:54 PM1/27/16

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Hello, I'm a new Cytoscape user and I'm having trouble creating standardized images from the networks in Cytoscape. I have a series of neworks that have identical nodes, but different edges. I need to export images of these networks that have the locations of the nodes in locations that are identical down to the pixel. I am using the LayoutSaver/LayoutMapper addon to map the locations of the nods.

What I need is a way to lock or set the exact level of zoom and center location for the window; eyeballing the location and zoom is insufficient for my purposes.

Additionally, the size of the output images should be identical.

Since the images created by Cytoscape seem to be wholly dependent on the image in the window, and not the network, I'm completely stumped at how to achieve the precision I need. If this program is incapable of producing the images I need, that's fine, I just need to know so I can stop wasting time on this pursuit and find another package for visualizing my networks.

Thanks in advance.

-WJL

Kei

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Jan 28, 2016, 12:15:54 PM1/28/16

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Hi.

It's a bit odd, but you can set all of zoom level and center of the network by using bypass. Here is how:

- Click "Style" tab

- Click "Network" tab on the bottom

- Select "Show all" menu item under "Properties"

- Then you can see all options like the screenshot above.

- Now you can set "Scale factor" and "Center x/y location" bypass values.

If you need fixed values for these, you can directly type-in numbers here and tweak the view.