Shapes as annotations - Githubissues

wikipathways / cytoscape-wikipathways-app

WikiPathways app for Cytoscape to open and access pathways from WikiPathways

Apache License 2.0

5 stars 7 forks source link

Shapes as annotations #44

Closed AlexanderPico closed 6 years ago

AlexanderPico commented 6 years ago

Remaining issues:

[x] Missing edges (WP254)
[x] Line thickness and color (WP254)
[x] SR shape is wrong (WP2118)
[ ] half cirlce shape is wrong (WP2118)
[x] fill color missing (WP2118)
[x] No longer on background canvac (WP254)
[x] Cell compartment and nucleus also should be annotations (WP2118)
[ ] Annotations need to be rotated (WP2118)

AlexanderPico commented 6 years ago

Complete list of shapes to convert to background annotations:

Cell Nucleus ER Golgi Mitochondria SR Organelle Vesicle Extracellular

Do not covert Groups (octagons) as they will certainly have edges connected to them and do not have a significant overlap with edges, like the case with the compartments above. Groups are definitely nodes.

AlexanderPico commented 6 years ago

Strategy for cell component shapes: Do all of them in the exact same way you did mitochondria, i.e., as custom annotation shapes. So, even though Nucleus appears like an Oval, don't use Oval Annotation Shapes. Let's just define the paths for these and then send them to Cytoscape the exact same way you do for mitochondria.

AlexanderPico commented 6 years ago

@AdamStuart Here's how it's done in PathVisio-Java https://github.com/PathVisio/pathvisio/blob/master/modules/org.pathvisio.core/src/org/pathvisio/core/view/GenMAPPShapes.java

AlexanderPico commented 6 years ago

How to rotate a General Path: http://www.javadocexamples.com/java_source/org/jfree/chart/needle/PointerNeedle.java.html

AdamStuart commented 6 years ago

Issue 48 Rotations created for outstanding items