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PathVisio / pathvisio

PathVisio - pathway editor, visualization and analysis software
http://www.pathvisio.org
Apache License 2.0
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New feature: Have PathVisio bring all data nodes to the front before saving, for each pathway #192

Open khanspers opened 1 year ago

khanspers commented 1 year ago

There is a known bug with svg generation, in summary:

"The order of objects in the SVG matters for things like clicking. If a group object is listed after all or most of the member nodes in the svg, you can't click the individual nodes because you are basically clicking the box and not the node underneath. Similarly, for elbow interactions, if they are drawn after one or more nodes, their path blocks the underlying nodes from clicks as well. The results is that in some pathways, some nodes are not clickable in the svg." (adapted from Alex's description).

This is solved by bringing all data nodes to the front in PathVisio.

Proposed feature: Add a feature to PathVisio to automatically place all nodes above in every pathway right before "save" operations. The manual steps that solve this issue are:

  1. Open pathways in PV
  2. Select all data nodes (Right-click, Select > Select all DataNodes)
  3. Right-click on a node (with all nodes selected) and choose Order > Bring to front.
DeniseSl22 commented 1 year ago

But, might there be a reason for people to have one DataNode behind another one? If not, then all DataNodes should be placed in the front anyway....

mkutmon commented 1 year ago

I'll check if I can fix that and make another release after I am back from my vacation!

mkutmon commented 1 year ago

and we should advise users against putting data nodes on top of each other :)