Add notebook for visualizing projections with PyVis by adamnsch · Pull Request #766 · neo4j/graph-data-science-client

adamnsch · 2024-10-15T14:18:57Z

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adamnsch · 2024-10-15T14:23:30Z

doc/modules/ROOT/pages/tutorials/visualize-with-pyvis.adoc

+[source, python, role=no-test]
+----
+net = Network(notebook = True,
+cdn_resources="remote",


I thought ruff would fix this ugly indentation?

should be able to format notebooks according to https://docs.astral.sh/ruff/configuration/#jupyter-notebook-discovery

issue with our setup .. see #768

I tried after rebasing on main, but the formatting issue remains the same after running makestyle locally

likely wrong pandoc version installed locally.

adamnsch · 2024-10-15T14:27:11Z

It would be nice to include either a html or image for the visualization in the docs somehow...

adamnsch · 2024-10-15T14:35:34Z

What the visualization looks like :)

FlorentinD

Nice start!

Looking forward to extend this notebook with other options.

README.md

doc/modules/ROOT/pages/tutorials/visualize-with-pyvis.adoc

FlorentinD · 2024-10-15T14:37:51Z

doc/modules/ROOT/pages/tutorials/visualize-with-pyvis.adoc

+[source, python, role=no-test]
+----
+net = Network(notebook = True,
+cdn_resources="remote",


should be able to format notebooks according to https://docs.astral.sh/ruff/configuration/#jupyter-notebook-discovery

doc/modules/ROOT/pages/tutorials/visualize-with-pyvis.adoc

FlorentinD · 2024-10-15T16:34:45Z

looked a bit into the convert.sh complain ... resulted in #767 use the correct version in dev.txt

adamnsch · 2024-10-16T07:21:18Z

looked a bit into the convert.sh complain ... resulted in #767 use the correct version in dev.txt

Ok, nice! I will have a look

Co-Authored-By: Florentin Dörre <[email protected]>

FlorentinD · 2024-10-17T08:02:12Z

doc/modules/ROOT/pages/tutorials/visualize-with-pyvis.adoc

+Unsuprisingly we can see that papers largely seem clustered by academic
+subject. We also note that some nodes appear larger in size, indicating


just the visualization does not explain to us what the academic subjects are right?
How about we add the subject as a label?

FlorentinD · 2024-10-18T07:40:58Z

@adamnsch updated pandoc on CI -> the checkstyle should go green now 🤞

adamnsch · 2024-10-18T07:41:37Z

@adamnsch updated pandoc on CI -> the checkstyle should go green now 🤞

Excellent work 👏

orazve · 2024-10-22T12:11:10Z

doc/modules/ROOT/pages/tutorials/visualize.adoc

+= Visualizing GDS Projections
+
+
+https://colab.research.google.com/github/neo4j/graph-data-science-client/blob/main/examples/import-sample-export-gnn.ipynb[image:https://colab.research.google.com/assets/colab-badge.svg[Open


is it a wrong link?

FlorentinD

Good idea to pull the logic into a graph method for convenience

FlorentinD · 2024-10-18T13:34:02Z

graphdatascience/graph/graph_object.py

+            an interactive graphical visualization of the specified graph
+        """
+
+        actual_node_properties = list(chain.from_iterable(self.node_properties().to_dict().values()))


can reduce it to set()

FlorentinD · 2024-10-28T08:29:54Z

graphdatascience/graph/graph_object.py

+        if visual_graph != self._name:
+            self._query_runner.call_procedure(
+                endpoint="gds.graph.drop",
+                params=CallParameters(graph_name=visual_graph),
+                custom_error=False,
+            )
+        elif clean_up_size_prop:
+            self._query_runner.call_procedure(
+                endpoint="gds.graph.nodeProperties.drop",
+                params=CallParameters(graph_name=visual_graph, nodeProperties=size_property),
+                custom_error=False,
+            )


I would suggest to have its own Graph.sample method and warn if the graph is too big.
Would avoid side-effect, the user is not aware off.

FlorentinD · 2024-10-28T08:41:28Z

graphdatascience/graph/graph_object.py

        ]
        return f"{self.__class__.__name__}({self._graph_info(yields=yield_fields).to_dict()})"
+
+    def visualize(


i like the idea of this.
maybe we can have different backends to be used?
pyvis/nvl? (with default to nvl)

should have a thought on the dependency. Likely similar optional dependency as for networkx

FlorentinD · 2024-10-28T08:44:26Z

#772 is the PR to allow replacing outputs for the doc version. Not yet ready but closing in :)

FlorentinD · 2025-11-04T16:26:58Z

that has been quite a journey 🚂
Now we have a dedicated python package neo4j-viz

closing in favor of #987

Add notebook for visualizing projections with PyVis

a696278

adamnsch force-pushed the visualize-notebook branch from 450af65 to a696278 Compare October 15, 2024 14:19

adamnsch commented Oct 15, 2024

View reviewed changes

FlorentinD requested changes Oct 15, 2024

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adamnsch and others added 2 commits October 16, 2024 14:17

Address review comments

fe47d91

Co-Authored-By: Florentin Dörre <[email protected]>

WIP

090f008

adamnsch force-pushed the visualize-notebook branch from 86cb0cd to 090f008 Compare October 17, 2024 07:38

FlorentinD reviewed Oct 17, 2024

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adamnsch added 2 commits October 17, 2024 11:05

Add G.visualize() method

3982faa

Add node coloring by label for G.visualize

5575cf3

adamnsch added 2 commits October 18, 2024 09:57

Add more info when hovering node for G.visualize

1498df5

Add more features to G.visualize

41f5f1f

adamnsch force-pushed the visualize-notebook branch from d121e3c to 511a18b Compare October 18, 2024 12:02

adamnsch added 2 commits October 18, 2024 14:55

Even more features for G.visualize

b01e44c

Add some G.visualize example calls to notebook

0703121

adamnsch force-pushed the visualize-notebook branch from 511a18b to 0703121 Compare October 18, 2024 12:55

orazve reviewed Oct 22, 2024

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FlorentinD mentioned this pull request Oct 22, 2024

Allow Notebook output to be preserved #771

Merged

FlorentinD reviewed Oct 28, 2024

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FlorentinD closed this Nov 4, 2025

		Unsuprisingly we can see that papers largely seem clustered by academic
		subject. We also note that some nodes appear larger in size, indicating

		= Visualizing GDS Projections


		https://colab.research.google.com/github/neo4j/graph-data-science-client/blob/main/examples/import-sample-export-gnn.ipynb[image:https://colab.research.google.com/assets/colab-badge.svg[Open

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