booldog.utils.cytoscape_utils

Helpers for exporting Cytoscape network views to image files via py4cytoscape. Requires a running Cytoscape instance (with the CyREST API reachable) to talk to.

Functions

export_network(suid, filename[, format, ...])

Export a Cytoscape network view to an image file.

Module Contents

booldog.utils.cytoscape_utils.export_network(suid, filename, format='png', overwrite_file=True, zoom=200)

Export a Cytoscape network view to an image file.

Fits the view to its content, clears any node/edge selection (so selection highlighting does not show up in the exported image), and exports the current view of the network identified by suid via py4cytoscape.network_views.export_image.

Parameters:

  • suid (int or str) – The Cytoscape network SUID (or, per py4cytoscape convention, a network name) identifying the network/view to export.

  • filename (str or Path) – Path of the image file to write. Coerced to str before being passed on to py4cytoscape.

  • format (str, default "png") – Image format to export, passed as py4cytoscape’s type argument (e.g. “png”, “pdf”, “svg”, …).

  • overwrite_file (bool, default True) – Whether to overwrite filename if it already exists.

  • zoom (int, default 200) – Zoom percentage applied to the exported image.

Return type:

None

Notes

py4cytoscape.network_views.fit_content fits the view to node positions only: it ignores edges/edge labels that extend beyond node boundaries, so such elements can be clipped in the exported image. This is a known Cytoscape limitation (reported as CSD-979); the Cytoscape developers’ response was “won’t fix”.