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https://github.com/flekschas/jupyter-scatter-tutorial
Jupyter Scatter Tutorial (that was first presented at SciPy '23)
https://github.com/flekschas/jupyter-scatter-tutorial
data-visualization embeddings jupyter-widget jupyterlab python scatter-plot
Last synced: about 2 months ago
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Jupyter Scatter Tutorial (that was first presented at SciPy '23)
- Host: GitHub
- URL: https://github.com/flekschas/jupyter-scatter-tutorial
- Owner: flekschas
- License: apache-2.0
- Created: 2023-06-21T15:32:21.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-09-17T17:35:42.000Z (3 months ago)
- Last Synced: 2024-09-17T21:58:49.168Z (3 months ago)
- Topics: data-visualization, embeddings, jupyter-widget, jupyterlab, python, scatter-plot
- Language: Jupyter Notebook
- Homepage: https://colab.research.google.com/github/flekschas/jupyter-scatter-tutorial/blob/main/notebooks/Index.ipynb
- Size: 7.9 MB
- Stars: 19
- Watchers: 4
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
# Jupyter Scatter Tutorial
:wave: Welcome! Here you will find the notebooks for the **Jupyter Scatter** tutorial, first presented at [SciPy 2023](https://cfp.scipy.org/2023/talk/AXSVZ3/). These notebooks offer an in-depth guide to interactive scatter plot visualizations using [`jupyter-scatter`](https://github.com/flekschas/jupyter-scatter). Specifically, the tutorial covers
1. [How to get started with Jupyter Scatter and visualize medium to large-scale datasets as interactive scatter plots.](notebooks/1-Getting-Started.ipynb)
2. [How to compose and link/synchronize multiple scatter plots](notebooks/2-Composing-Linking-Scatter-Plots.ipynb)
3. How to integrate Jupyter Scatter with other widgets to build bespoke interfaces for:
1. [Exploring LLM-based sentence embeddings](notebooks/3-LLM-Sentence-Embedding.ipynb)
2. [Comparing multiple embedding method of the Fashion MNIST dataset](notebooks/3-Fashion-MNIST.ipynb)
3. [Browsing genomic data with HiGlass and loci embeddings](notebooks/3-Genomics.ipynb)
4. [Comparing a pair of single-cell embeddings by their label abundance differences](notebooks/3-Comparative-Single-Cell-Embeddings.ipynb)
4. How to use the tooltip feature, introduced in `v0.15.0` (Added after the SciPy 2023):
1. [Tooltip with text previews for the LLM-based sentence embeddings](notebooks/4-Tooltip-LLM-Sentence-Embedding.ipynb)
2. [Tooltip with image previews for the Fashion MNIST embedding](notebooks/4-Tooltip-Fashion-MNIST.ipynb)
3. [Tooltip for a single-cell embededding](notebooks/4-Tooltip-Single-Cell-Embeddings.ipynb)
4. [Tooltip with audio previews for Google's Magenta Nsynth dataset](notebooks/4-Tooltip-Google-Nsynth.ipynb)
5. How to add features to Jupyter Scatter through composition with other Jupyter Widgets or other Python libraries (Added after the SciPy 2023):
1. [Search](notebooks/5-Search.ipynb)
2. [Cluster Outlines and Contours](notebooks/5-Cluster-Outlines-Contours.ipynb)
> **Note**
>
> You can find my [SciPy '23 talk on YouTube](https://www.youtube.com/watch?v=RyC5ixtQG-Q) and the accompanying [slides at Speaker Deck](https://speakerdeck.com/flekschas/interactive-exploration-of-large-scale-datasets-with-jupyter-scatter).
## Run the Tutorial
#### Online
If you have a Google/Gmail account, you can run this tutorial from your browser using Colab: [](https://colab.research.google.com/github/flekschas/jupyter-scatter-tutorial/blob/main/notebooks/Index.ipynb).
> [!IMPORTANT]
> You need to manually install Jupyter Scatter when running the notebooks in Google Colab via `!pip install jupyter-scatter`. Make sure to **not** install `jscatter` as that is a different package.
#### Locally
To run the notebook locally we recommend setting up a custom environment using [hatch](https://github.com/pypa/hatch) as follows:
```sh
hatch shell
```
Finally, you can now run the notebooks with:
```sh
jupyterlab
```