Metadata-Version: 2.3
Name: jupyter-scatter
Version: 0.16.1
Summary: An interactive scatter plot widget for Jupyter Notebook, Lab, and Google Colab that can handle millions of points and supports view linking
Project-URL: homepage, https://jupyter-scatter.dev
Project-URL: documentation, https://jupyter-scatter.dev/api
Project-URL: repository, https://github.com/flekschas/jupyter-scatter
Project-URL: changelog, https://github.com/flekschas/jupyter-scatter/blob/main/CHANGELOG.md
Author-email: Fritz Lekschas <code@lekschas.de>
License: Apache-2.0
License-File: LICENSE
Keywords: ipython,ipywidgets,jupyter,jupyterlab,jupyterlab-extension,scatter,scatter plot,widgets
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Multimedia :: Graphics
Requires-Dist: anywidget>=0.2.0
Requires-Dist: ipython
Requires-Dist: ipywidgets<9,>=7.6
Requires-Dist: matplotlib
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: traittypes>=0.2.1
Requires-Dist: typing-extensions
Provides-Extra: dev
Requires-Dist: anywidget[dev]; extra == 'dev'
Requires-Dist: black[jupyter]; extra == 'dev'
Requires-Dist: jupyterlab; extra == 'dev'
Requires-Dist: pytest; extra == 'dev'
Requires-Dist: ruff; extra == 'dev'
Description-Content-Type: text/markdown

<h1 align="center">
  <img src="https://jupyter-scatter.dev/images/logo-dark.svg" height="24"></img> Jupyter Scatter
</h1>

<div align="center">
  
  [![pypi version](https://img.shields.io/pypi/v/jupyter-scatter.svg?color=1a8cff&style=flat-square)](https://pypi.org/project/jupyter-scatter/)
  [![build status](https://img.shields.io/github/actions/workflow/status/flekschas/jupyter-scatter/build.yml?branch=master&color=1a8cff&style=flat-square)](https://github.com/flekschas/jupyter-scatter/actions?query=workflow%3A%22Build+Python+%26+JavaScript%22)
  [![API docs](https://img.shields.io/badge/API-docs-1a8cff.svg?style=flat-square)](https://jupyter-scatter.dev/api)
  [![notebook examples](https://img.shields.io/badge/notebook-examples-1a8cff.svg?style=flat-square)](notebooks/get-started.ipynb)
  [![tutorial](https://img.shields.io/badge/SciPy_'23-tutorial-1a8cff.svg?style=flat-square)](https://github.com/flekschas/jupyter-scatter-tutorial)
  
</div>

<div align="center">
  
  <strong>An interactive scatter plot widget for Jupyter Notebook, Lab, and Google Colab</strong><br/>that can handle [millions of points](#visualize-millions-of-data-points) and supports [view linking](#linking-scatter-plots).
  
</div>

<br/>

<div align="center">
  
  ![Demo](https://user-images.githubusercontent.com/932103/223292112-c9ca18b9-bc6b-4c3b-94ac-984960e8f717.gif)
  
</div>

**Features?**

- 🖱️ **Interactive**: Pan, zoom, and select data points interactively with your mouse or through the Python API.
- 🚀 **Scalable**: Plot up to several millions data points smoothly thanks to WebGL rendering.
- 🔗 **Interlinked**: Synchronize the view, hover, and selection across multiple scatter plot instances.
- ✨ **Effective Defaults**: Rely on Jupyter Scatter to choose perceptually effective point colors and opacity by default.
- 📚 **Friendly API:** Enjoy a readable API that integrates deeply with Pandas DataFrames.
- 🛠️ **Integratable**: Use Jupyter Scatter in your own widgets by observing its traitlets.

**Why?**

Imagine trying to explore a dataset of millions of data points as a 2D scatter. Besides plotting, the exploration typically involves three things: First, we want to interactively adjust the view (e.g., via panning & zooming) and the visual point encoding (e.g., the point color, opacity, or size). Second, we want to be able to select and highlight data points. And third, we want to compare multiple datasets or views of the same dataset (e.g., via synchronized interactions). The goal of jupyter-scatter is to support all three requirements and scale to millions of points.

**How?**

Internally, Jupyter Scatter uses [regl-scatterplot](https://github.com/flekschas/regl-scatterplot/) for WebGL rendering, [traitlets](https://traitlets.readthedocs.io/en/stable/) for two-way communication between the JS and iPython kernels, and [anywidget](https://anywidget.dev/) for composing the widget.

**Index**

1. [Install](#install)
2. [Get Started](#get-started)
3. [Docs](https://jupyter-scatter.dev)
4. [Examples](notebooks/examples.ipynb)
5. [Development](#development)

## Install

```bash
pip install jupyter-scatter
```

If you are using JupyterLab <=2:

```bash
jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter-scatter
```

For a minimal working example, take a look at [test-environments](test-environments).

## Get Started

> [!TIP]
> Visit [jupyter-scatter.dev](https://jupyter-scatter.dev) for details on all essential features of Jupyter Scatter and check out our [full-blown tutorial](https://github.com/flekschas/jupyter-scatter-tutorial) from SciPy '23.

#### Simplest Example

In the simplest case, you can pass the x/y coordinates to the plot function as follows:

```python
import jscatter
import numpy as np

x = np.random.rand(500)
y = np.random.rand(500)

jscatter.plot(x, y)
```

<img width="448" alt="Simplest scatter plotexample" src="https://user-images.githubusercontent.com/932103/116143120-bc5f2280-a6a8-11eb-8614-51def74d692e.png">

#### Pandas Example

Say your data is stored in a Pandas dataframe like the following:

```python
import pandas as pd

# Just some random float and int values
data = np.random.rand(500, 4)
df = pd.DataFrame(data, columns=['mass', 'speed', 'pval', 'group'])
# We'll convert the `group` column to strings to ensure it's recognized as
# categorical data. This will come in handy in the advanced example.
df['group'] = df['group'].map(lambda c: chr(65 + round(c)), na_action=None)
```

|   | x    | y    | value | group |
|---|------|------|-------|-------|
| 0 |	0.13 | 0.27 | 0.51  | G     |
| 1 |	0.87 | 0.93 | 0.80  | B     |
| 2 |	0.10 | 0.25 | 0.25  | F     |
| 3 |	0.03 | 0.90 | 0.01  | G     |
| 4 |	0.19 | 0.78 | 0.65  | D     |

You can then visualize this data by referencing column names:

```python
jscatter.plot(data=df, x='mass', y='speed')
```

<details><summary>Show the resulting scatter plot</summary>
<img width="448" alt="Pandas scatter plot example" src="https://user-images.githubusercontent.com/932103/116143383-1364f780-a6a9-11eb-974c-4facec249974.png">
</details>

#### Advanced example

Often you want to customize the visual encoding, such as the point color, size, and opacity.

```python
jscatter.plot(
  data=df,
  x='mass',
  y='speed',
  size=8, # static encoding
  color_by='group', # data-driven encoding
  opacity_by='density', # view-driven encoding
)
```

<img width="448" alt="Advanced scatter plot example" src="https://user-images.githubusercontent.com/932103/116143470-2f689900-a6a9-11eb-861f-fcd8c563fde4.png">

In the above example, we chose a static point size of `8`. In contrast, the point color is data-driven and assigned based on the categorical `group` value. The point opacity is view-driven and defined dynamically by the number of points currently visible in the view.

Also notice how jscatter uses an appropriate color map by default based on the data type used for color encoding. In this examples, jscatter uses the color blindness safe color map from [Okabe and Ito](https://jfly.uni-koeln.de/color/#pallet) as the data type is `categorical` and the number of categories is less than `9`.

**Important:** in order for jscatter to recognize categorical data, the `dtype` of the corresponding column needs to be `category`!

You can, of course, customize the color map and many other parameters of the visual encoding as shown next.

#### Functional API Example

The [flat API](#advanced-example) can get overwhelming when you want to customize a lot of properties. Therefore, jscatter provides a functional API that groups properties by type and exposes them via meaningfully-named methods.

```python
scatter = jscatter.Scatter(data=df, x='mass', y='speed')
scatter.selection(df.query('mass < 0.5').index)
scatter.color(by='mass', map='plasma', order='reverse')
scatter.opacity(by='density')
scatter.size(by='pval', map=[2, 4, 6, 8, 10])
scatter.height(480)
scatter.background('black')
scatter.show()
```

<img width="448" alt="Functional API scatter plot example" src="https://user-images.githubusercontent.com/932103/116155554-3945c880-a6b8-11eb-9033-4d0c07f01590.png">

When you update properties dynamically, i.e., after having called `scatter.show()`, the plot will update automatically. For instance, try calling `scatter.xy('speed', 'mass')`and you will see how the points are mirrored along the diagonal.

Moreover, all arguments are optional. If you specify arguments, the methods will act as setters and change the properties. If you call a method without any arguments it will act as a getter and return the property (or properties). For example, `scatter.selection()` will return the _currently_ selected points.

Finally, the scatter plot is interactive and supports two-way communication. Hence, if you select some point with the lasso tool and then call `scatter.selection()` you will get the current selection.

#### Linking Scatter Plots

To explore multiple scatter plots and have their view, selection, and hover interactions link, use `jscatter.link()`.

```python
jscatter.link([
  jscatter.Scatter(data=embeddings, x='pcaX', y='pcaY', **config),
  jscatter.Scatter(data=embeddings, x='tsneX', y='tsneY', **config),
  jscatter.Scatter(data=embeddings, x='umapX', y='umapY', **config),
  jscatter.Scatter(data=embeddings, x='caeX', y='caeY', **config)
], rows=2)
```

https://user-images.githubusercontent.com/932103/162584133-85789d40-04f5-428d-b12c-7718f324fb39.mp4

See [notebooks/linking.ipynb](notebooks/linking.ipynb) for more details.

#### Visualize Millions of Data Points

With `jupyter-scatter` you can easily visualize and interactively explore datasets with millions of points.

In the following we're visualizing 5 million points generated with the [Rössler attractor](https://en.wikipedia.org/wiki/R%C3%B6ssler_attractor).

```python
points = np.asarray(roesslerAttractor(5000000))
jscatter.plot(points[:,0], points[:,1], height=640)
```

https://user-images.githubusercontent.com/932103/162586987-0b5313b0-befd-4bd1-8ef5-13332d8b15d1.mp4

See [notebooks/examples.ipynb](notebooks/examples.ipynb) for more details.

#### Google Colab

While jscatter is primarily developed for Jupyter Lab and Notebook, it also runs just fine in Google Colab. See [jupyter-scatter-colab-test.ipynb](https://colab.research.google.com/drive/195z6h6LsYpC25IIB3fSZIVUbqVlhtnQo?usp=sharing) for an example.

---

### Development

<details><summary>Setting up a development environment</summary>
<p>

**Requirements:**

- [Hatch](https://hatch.pypa.io/latest/) >= 1.7.0

**Installation:**

```bash
git clone https://github.com/flekschas/jupyter-scatter/ jscatter && cd jscatter
hatch shell
pip install -e ".[dev]"
```

**After Changing Python code:** restart the kernel.

Alternatively, you can enable auto reloading by enabling the `autoreload`
extension. To do so, run the following code at the beginning of a notebook:

```py
%load_ext autoreload
%autoreload 2
```

**After Changing JavaScript code:** do `cd js && npm run build`.

Alternatively, you can run `npm run watch` and rebundle the code on the fly.

</p>
</details>

<details><summary>Setting up a test environment</summary>
<p>

Go to [test-environments](test-environments) and follow the instructions.

</p>
</details>
