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import marimo as mo
import marimo as mo
Temporal Network Visualizations with Manim¶
Prerequisites¶
First, we need to set up our Python environment that has PyTorch, PyTorch Geometric and PathpyG installed. Depending on where you are executing this notebook, this might already be (partially) done. E.g. Google Colab has PyTorch installed by default so we only need to install the remaining dependencies. The DevContainer that is part of our GitHub Repository on the other hand already has all of the necessary dependencies installed.
In the following, we install the packages for usage in Google Colab using Jupyter magic commands. For other environments comment in or out the commands as necessary. For more details on how to install pathpyG especially if you want to install it with GPU-support, we refer to our documentation. Note that %%capture discards the full output of the cell to not clutter this tutorial with unnecessary installation details. If you want to print the output, you can comment %%capture out.
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# %%capture
# # !pip install torch
# !pip install torch_geometric
# !pip install git+https://github.com/pathpy/pathpyG.git
# %%capture
# # !pip install torch
# !pip install torch_geometric
# !pip install git+https://github.com/pathpy/pathpyG.git
Note that using the Manim-backend in PathpyG requires the installation of Manim. It will not be automatically installed with PathpyG due to its additional dependencies. We recommend using the installation instructions in the Manim documentation or our provided DevContainer.
Motivation and Learning Objectives¶
While you already learned how to visualise graphs with PathpyG in the interactive graph visualisation tutorial, those visualisations mostly considered static graphs.
In this tutorial, you will learn how to use the Manim backend in PathpyG to generate videos (.mp4) or animations (.gif) of temporal graphs.
Let's Get Started¶
We need to import PathpyG first:
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import os
import tempfile
import pathpyG as pp
import os
import tempfile
import pathpyG as pp
Next, we can create a temporal graph that we want to visualise:
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t = pp.TemporalGraph.from_edge_list(
[
("a", "b", 1),
("b", "c", 5),
("c", "d", 9),
("d", "a", 9),
("a", "b", 10),
("b", "c", 10),
("a", "b", 8),
("b", "c", 13),
("c", "d", 17),
("d", "a", 19),
("a", "b", 20),
("b", "c", 18),
]
)
t = pp.TemporalGraph.from_edge_list(
[
("a", "b", 1),
("b", "c", 5),
("c", "d", 9),
("d", "a", 9),
("a", "b", 10),
("b", "c", 10),
("a", "b", 8),
("b", "c", 13),
("c", "d", 17),
("d", "a", 19),
("a", "b", 20),
("b", "c", 18),
]
)
The plot function using Manim as backend allows to use a variety of customization options to visualize temporal graphs and outputs a video. Some examples are provided below, e.g. the node_size or the edge_size.
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pp.plot(t, backend="manim", node_size=20, edge_size=10, edge_color="red", node_color="gray");
pp.plot(t, backend="manim", node_size=20, edge_size=10, edge_color="red", node_color="gray");
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The videos can be exported as .mp4 or .gif if you provide a filename to the plot function.
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# Cell tags: skip-execution
with tempfile.TemporaryDirectory() as tmpdirname:
tmp_path = os.path.join(tmpdirname, "temporal_graph_manim.gif")
pp.plot(
t,
backend="manim",
node_size=20,
edge_size=4,
edge_color="red",
node_color="gray",
filename=tmp_path,
)
print(f"Animation saved to {tmp_path}")
print(f"Files in temp dir: {os.listdir(tmpdirname)}")
# Cell tags: skip-execution
with tempfile.TemporaryDirectory() as tmpdirname:
tmp_path = os.path.join(tmpdirname, "temporal_graph_manim.gif")
pp.plot(
t,
backend="manim",
node_size=20,
edge_size=4,
edge_color="red",
node_color="gray",
filename=tmp_path,
)
print(f"Animation saved to {tmp_path}")
print(f"Files in temp dir: {os.listdir(tmpdirname)}")
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Animation 89: Uncreate(LabeledDot), etc.: 28%|██▊ | 17/60 [00:00<00:00, 164.66it/s]
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Animation saved to /tmp/tmpfbezr8tt/temporal_graph_manim.gif Files in temp dir: ['temporal_graph_manim.gif']
Dynamic Customisations and Layout¶
Since we use manim to animate temporal networks, we can also use dynamic customisations that change over time. For example, we can change the node_size or edge_size over time.
To change those properties dynamically, we can provide a dictionary that maps node/source-target id and the time step to the desired property value.
Additionally, we can use dynamic layouts that are based on sliding windows. For example, we can use a ForceAtlas2 layout that is computed based on a sliding window of the last 3 time steps. This allows us to have a layout that changes over time but is still stable enough to be visually appealing.
The following shows an example where all of the customisations described above are used:
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# Cell tags: skip-execution
pp.plot(
t,
backend="manim",
layout_window_size=[3, 1],
layout="fa2",
node_size=12,
edge_color={("b", "c", 10): "green"},
node_color={("a", 3): "yellow", ("a", 0): "green", ("b", 3): "black"},
);
# Cell tags: skip-execution
pp.plot(
t,
backend="manim",
layout_window_size=[3, 1],
layout="fa2",
node_size=12,
edge_color={("b", "c", 10): "green"},
node_color={("a", 3): "yellow", ("a", 0): "green", ("b", 3): "black"},
);
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Real-World Example¶
As a final example, we show how to visualise a real-world temporal graph with Manim. We use Netschleuder Online Repository (see our tutorial Graph Learning in Netzschleuder Data for more information) to obtain a temporal interaction graph between baboons and color the types of interactions in different colors.
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g = pp.io.read_netzschleuder_graph('sp_baboons', 'observational', time_attr='time')
g = pp.io.read_netzschleuder_graph('sp_baboons', 'observational', time_attr='time')
The timestamps are provided in seconds since epoch (converted from unix time). We first convert them to a more human-readable format (12-hour intervals since the first interaction):
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g.data.time -= g.data.time.min()
g.data.time = g.data.time // (60 * 60 * 12) # convert to 12 hours intervals
g.data.time -= g.data.time.min()
g.data.time = g.data.time // (60 * 60 * 12) # convert to 12 hours intervals
The dataset contains different types of interactions between the baboons. We can use this information to color the edges based on the interaction type:
In [ ]:
Copied!
colors = []
for category in g.data["edge_category"]:
match category:
case "Affiliative":
colors.append("red")
case "Agonistic":
colors.append("green")
case "Other":
colors.append("grey")
colors = []
for category in g.data["edge_category"]:
match category:
case "Affiliative":
colors.append("red")
case "Agonistic":
colors.append("green")
case "Other":
colors.append("grey")
In [ ]:
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# Cell tags: skip-execution
pp.plot(
g,
backend="manim",
layout_window_size=12, # six days
layout="kk",
edge_color=colors,
edge_size=2.5,
delta=500, # Each time step is 500 ms
);
# Cell tags: skip-execution
pp.plot(
g,
backend="manim",
layout_window_size=12, # six days
layout="kk",
edge_color=colors,
edge_size=2.5,
delta=500, # Each time step is 500 ms
);
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