multiscoresplot 1.0.3__tar.gz → 1.0.6__tar.gz

multiscoresplot-1.0.6/.github/workflows/docs.yml

@@ -0,0 +1,27 @@
+name: Deploy Docs
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: astral-sh/setup-uv@v5
+        with:
+          python-version: "3.12"
+
+      - name: Configure git for gh-deploy
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+
+      - name: Deploy to GitHub Pages
+        run: uv run --group docs mkdocs gh-deploy --force

{multiscoresplot-1.0.3 → multiscoresplot-1.0.6}/.pre-commit-config.yaml

@@ -10,6 +10,7 @@ repos:
       - id: check-toml
       - id: check-added-large-files
         args: ["--maxkb=500"]
+        exclude: '^uv\.lock$'
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.9.9

{multiscoresplot-1.0.3 → multiscoresplot-1.0.6}/PKG-INFO

@@ -1,10 +1,11 @@
 Metadata-Version: 2.4
 Name: multiscoresplot
-Version: 1.0.3
+Version: 1.0.6
 Summary: Multi-dimensional gene set scoring and visualization for single-cell transcriptomics
-Project-URL: Homepage, https://github.com/andrecmacedo/multiscoresplot
-Project-URL: Repository, https://github.com/andrecmacedo/multiscoresplot
-Project-URL: Issues, https://github.com/andrecmacedo/multiscoresplot/issues
+Project-URL: Homepage, https://github.com/AndreMacedo88/multiscoresplot
+Project-URL: Documentation, https://AndreMacedo88.github.io/multiscoresplot/
+Project-URL: Repository, https://github.com/AndreMacedo88/multiscoresplot
+Project-URL: Issues, https://github.com/AndreMacedo88/multiscoresplot/issues
 Author: Andre Macedo
 License-Expression: MIT
 License-File: LICENSE
@@ -33,9 +34,10 @@ Description-Content-Type: text/markdown
 # multiscoresplot
 
 [![CI](https://github.com/AndreMacedo88/multiscoresplot/actions/workflows/ci.yml/badge.svg)](https://github.com/AndreMacedo88/multiscoresplot/actions/workflows/ci.yml)
-[![PyPI](https://img.shields.io/pypi/v/multiscoresplot)](https://pypi.org/project/multiscoresplot/)
+[![Docs](https://img.shields.io/badge/docs-GitHub%20Pages-blue)](https://AndreMacedo88.github.io/multiscoresplot/)
+[![PyPI](https://img.shields.io/pypi/v/multiscoresplot?cacheSeconds=3600)](https://pypi.org/project/multiscoresplot/)
+[![Python](https://img.shields.io/pypi/pyversions/multiscoresplot?cacheSeconds=3600)](https://pypi.org/project/multiscoresplot/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
-[![Python](https://img.shields.io/pypi/pyversions/multiscoresplot)](https://pypi.org/project/multiscoresplot/)
 
 **Multi-dimensional gene set scoring and visualization for single-cell transcriptomics.**
 
@@ -83,7 +85,7 @@ msp.plot_embedding(
 
 ## Pipeline
 
-multiscoresplot follows a 5-step pipeline:
+multiscoresplot follows a 3-step pipeline:
 
 ### Step 1 — Score gene sets
 
@@ -102,9 +104,11 @@ scores = msp.score_gene_sets(
 )
 ```
 
-### Step 2 — Blend to RGB (2–3 gene sets)
+### Step 2 — Map scores to RGB
 
-For 2–3 gene sets, use multiplicative blending from white. Each gene set darkens toward its base color proportional to the score.
+Convert gene set scores into per-cell RGB colors. Two options depending on how many gene sets you want to visualize:
+
+**Blend (2–3 gene sets)** — multiplicative blending from white, where each gene set darkens toward its base color proportional to the score.
 
 ```python
 # Default colors (2 sets: blue/red, 3 sets: R/G/B)
@@ -114,9 +118,7 @@ rgb = msp.blend_to_rgb(scores)
 rgb = msp.blend_to_rgb(scores, colors=[(1, 0, 0), (0, 0.5, 1)])
 ```
 
-### Step 3 — Reduce to RGB (2+ gene sets)
-
-For any number of gene sets (2 or more), use dimensionality reduction to map scores to 3 RGB channels. Built-in methods: PCA, NMF, and ICA.
+**Reduce (2+ gene sets)** — dimensionality reduction maps scores to 3 RGB channels. Built-in methods: PCA, NMF, and ICA.
 
 ```python
 rgb = msp.reduce_to_rgb(scores, method="pca")  # default
@@ -124,7 +126,7 @@ rgb = msp.reduce_to_rgb(scores, method="nmf")
 rgb = msp.reduce_to_rgb(scores, method="ica")
 ```
 
-### Step 4 — Plot embedding
+### Step 3 — Plot embedding
 
 Scatter plot of embedding coordinates colored by RGB values, with an integrated color-space legend.
 
@@ -154,9 +156,7 @@ ax = msp.plot_embedding(
 )
 ```
 
-### Step 4b — Interactive plot (requires plotly)
-
-WebGL-accelerated Plotly scatter plot with hover info showing gene set scores, RGB channel values, and custom metadata.
+**Interactive plot (requires plotly)** — WebGL-accelerated scatter plot with hover info showing gene set scores, RGB channel values, and custom metadata.
 
 ```python
 msp.plot_embedding_interactive(
@@ -174,9 +174,9 @@ msp.plot_embedding_interactive(
 )
 ```
 
-### Step 5 — Standalone legend
+### Optional — Standalone legend
 
-Render the color-space legend on any matplotlib axes.
+The plotting functions above include an integrated legend by default. If you need to render the legend separately (e.g., for a custom figure layout):
 
 ```python
 import matplotlib.pyplot as plt
@@ -214,6 +214,15 @@ msp.register_reducer("umap", my_umap_reducer, component_prefix="UMAP")
 rgb = msp.reduce_to_rgb(scores, method="umap")
 ```
 
+## Documentation
+
+Full documentation is available at **[AndreMacedo88.github.io/multiscoresplot](https://AndreMacedo88.github.io/multiscoresplot/)**, including:
+
+- [Getting Started](https://AndreMacedo88.github.io/multiscoresplot/getting-started/) — installation and quick start
+- [Pipeline Guide](https://AndreMacedo88.github.io/multiscoresplot/pipeline/) — detailed pipeline tutorial
+- [API Reference](https://AndreMacedo88.github.io/multiscoresplot/api/) — full function signatures and parameters
+- [Examples](https://AndreMacedo88.github.io/multiscoresplot/examples/) — custom reducers, plot customization, and more
+
 ## API Reference
 
 | Function                                            | Description                               |
@@ -230,7 +239,7 @@ rgb = msp.reduce_to_rgb(scores, method="umap")
 ## Development
 
 ```bash
-git clone https://github.com/andrecmacedo/multiscoresplot.git
+git clone https://github.com/AndreMacedo88/multiscoresplot.git
 cd multiscoresplot
 
 # Install in editable mode with dev dependencies

{multiscoresplot-1.0.3 → multiscoresplot-1.0.6}/README.md

@@ -1,9 +1,10 @@
 # multiscoresplot
 
 [![CI](https://github.com/AndreMacedo88/multiscoresplot/actions/workflows/ci.yml/badge.svg)](https://github.com/AndreMacedo88/multiscoresplot/actions/workflows/ci.yml)
-[![PyPI](https://img.shields.io/pypi/v/multiscoresplot)](https://pypi.org/project/multiscoresplot/)
+[![Docs](https://img.shields.io/badge/docs-GitHub%20Pages-blue)](https://AndreMacedo88.github.io/multiscoresplot/)
+[![PyPI](https://img.shields.io/pypi/v/multiscoresplot?cacheSeconds=3600)](https://pypi.org/project/multiscoresplot/)
+[![Python](https://img.shields.io/pypi/pyversions/multiscoresplot?cacheSeconds=3600)](https://pypi.org/project/multiscoresplot/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
-[![Python](https://img.shields.io/pypi/pyversions/multiscoresplot)](https://pypi.org/project/multiscoresplot/)
 
 **Multi-dimensional gene set scoring and visualization for single-cell transcriptomics.**
 
@@ -51,7 +52,7 @@ msp.plot_embedding(
 
 ## Pipeline
 
-multiscoresplot follows a 5-step pipeline:
+multiscoresplot follows a 3-step pipeline:
 
 ### Step 1 — Score gene sets
 
@@ -70,9 +71,11 @@ scores = msp.score_gene_sets(
 )
 ```
 
-### Step 2 — Blend to RGB (2–3 gene sets)
+### Step 2 — Map scores to RGB
 
-For 2–3 gene sets, use multiplicative blending from white. Each gene set darkens toward its base color proportional to the score.
+Convert gene set scores into per-cell RGB colors. Two options depending on how many gene sets you want to visualize:
+
+**Blend (2–3 gene sets)** — multiplicative blending from white, where each gene set darkens toward its base color proportional to the score.
 
 ```python
 # Default colors (2 sets: blue/red, 3 sets: R/G/B)
@@ -82,9 +85,7 @@ rgb = msp.blend_to_rgb(scores)
 rgb = msp.blend_to_rgb(scores, colors=[(1, 0, 0), (0, 0.5, 1)])
 ```
 
-### Step 3 — Reduce to RGB (2+ gene sets)
-
-For any number of gene sets (2 or more), use dimensionality reduction to map scores to 3 RGB channels. Built-in methods: PCA, NMF, and ICA.
+**Reduce (2+ gene sets)** — dimensionality reduction maps scores to 3 RGB channels. Built-in methods: PCA, NMF, and ICA.
 
 ```python
 rgb = msp.reduce_to_rgb(scores, method="pca")  # default
@@ -92,7 +93,7 @@ rgb = msp.reduce_to_rgb(scores, method="nmf")
 rgb = msp.reduce_to_rgb(scores, method="ica")
 ```
 
-### Step 4 — Plot embedding
+### Step 3 — Plot embedding
 
 Scatter plot of embedding coordinates colored by RGB values, with an integrated color-space legend.
 
@@ -122,9 +123,7 @@ ax = msp.plot_embedding(
 )
 ```
 
-### Step 4b — Interactive plot (requires plotly)
-
-WebGL-accelerated Plotly scatter plot with hover info showing gene set scores, RGB channel values, and custom metadata.
+**Interactive plot (requires plotly)** — WebGL-accelerated scatter plot with hover info showing gene set scores, RGB channel values, and custom metadata.
 
 ```python
 msp.plot_embedding_interactive(
@@ -142,9 +141,9 @@ msp.plot_embedding_interactive(
 )
 ```
 
-### Step 5 — Standalone legend
+### Optional — Standalone legend
 
-Render the color-space legend on any matplotlib axes.
+The plotting functions above include an integrated legend by default. If you need to render the legend separately (e.g., for a custom figure layout):
 
 ```python
 import matplotlib.pyplot as plt
@@ -182,6 +181,15 @@ msp.register_reducer("umap", my_umap_reducer, component_prefix="UMAP")
 rgb = msp.reduce_to_rgb(scores, method="umap")
 ```
 
+## Documentation
+
+Full documentation is available at **[AndreMacedo88.github.io/multiscoresplot](https://AndreMacedo88.github.io/multiscoresplot/)**, including:
+
+- [Getting Started](https://AndreMacedo88.github.io/multiscoresplot/getting-started/) — installation and quick start
+- [Pipeline Guide](https://AndreMacedo88.github.io/multiscoresplot/pipeline/) — detailed pipeline tutorial
+- [API Reference](https://AndreMacedo88.github.io/multiscoresplot/api/) — full function signatures and parameters
+- [Examples](https://AndreMacedo88.github.io/multiscoresplot/examples/) — custom reducers, plot customization, and more
+
 ## API Reference
 
 | Function                                            | Description                               |
@@ -198,7 +206,7 @@ rgb = msp.reduce_to_rgb(scores, method="umap")
 ## Development
 
 ```bash
-git clone https://github.com/andrecmacedo/multiscoresplot.git
+git clone https://github.com/AndreMacedo88/multiscoresplot.git
 cd multiscoresplot
 
 # Install in editable mode with dev dependencies

multiscoresplot-1.0.6/docs/api/colorspace.md

@@ -0,0 +1,25 @@
+# Color Space
+
+Color mapping from gene set scores to RGB (pipeline steps 2–3).
+
+## Blending (2–3 gene sets)
+
+::: multiscoresplot.blend_to_rgb
+
+---
+
+## Dimensionality Reduction (2+ gene sets)
+
+::: multiscoresplot.reduce_to_rgb
+
+---
+
+## Custom Reducers
+
+::: multiscoresplot.register_reducer
+
+---
+
+## Utility
+
+::: multiscoresplot.get_component_labels

multiscoresplot-1.0.6/docs/api/index.md

@@ -0,0 +1,27 @@
+# API Reference
+
+## Overview
+
+| Function | Description | Pipeline Step |
+|----------|-------------|---------------|
+| [`score_gene_sets`](scoring.md) | Score gene sets per cell via pyUCell | Step 1 |
+| [`blend_to_rgb`](colorspace.md#multiscoresplot.blend_to_rgb) | Multiplicative blend to RGB (2–3 sets) | Step 2 |
+| [`reduce_to_rgb`](colorspace.md#multiscoresplot.reduce_to_rgb) | Dimensionality reduction to RGB (2+ sets) | Step 2 |
+| [`plot_embedding`](plotting.md) | Static matplotlib scatter plot | Step 3 |
+| [`plot_embedding_interactive`](interactive.md) | Interactive Plotly scatter plot | Step 3 |
+| [`render_legend`](legend.md) | Draw color-space legend on axes | Optional |
+| [`register_reducer`](colorspace.md#multiscoresplot.register_reducer) | Register a custom reduction method | Extensibility |
+| [`get_component_labels`](colorspace.md#multiscoresplot.get_component_labels) | Get axis labels for a reduction method | Utility |
+
+## Module Layout
+
+All public functions are available directly from the top-level `multiscoresplot` namespace:
+
+```python
+import multiscoresplot as msp
+
+msp.score_gene_sets(...)
+msp.blend_to_rgb(...)
+msp.reduce_to_rgb(...)
+msp.plot_embedding(...)
+```

multiscoresplot-1.0.6/docs/api/interactive.md

@@ -0,0 +1,8 @@
+# Interactive Plotting
+
+WebGL-accelerated Plotly scatter plot with hover metadata (pipeline step 4b).
+
+!!! note
+    Requires the `plotly` extra: `pip install 'multiscoresplot[interactive]'`
+
+::: multiscoresplot.plot_embedding_interactive

multiscoresplot-1.0.6/docs/api/legend.md

@@ -0,0 +1,5 @@
+# Legend
+
+Color-space legend rendering for matplotlib axes (pipeline step 5).
+
+::: multiscoresplot.render_legend

multiscoresplot-1.0.6/docs/api/plotting.md

@@ -0,0 +1,5 @@
+# Plotting
+
+Static matplotlib scatter plot of embeddings colored by RGB values (pipeline step 4).
+
+::: multiscoresplot.plot_embedding

multiscoresplot-1.0.6/docs/api/scoring.md

@@ -0,0 +1,5 @@
+# Scoring
+
+Gene set scoring via pyUCell (pipeline step 1).
+
+::: multiscoresplot.score_gene_sets

multiscoresplot-1.0.6/docs/changelog.md

@@ -0,0 +1,19 @@
+# Changelog
+
+## 1.0.3
+
+- Fix badge display in README
+
+## 1.0.2
+
+- Fix legend not being plotted in interactive "direct" methods
+- Fix CI badge path in README
+
+## 1.0.1
+
+- Initial stable release
+- 5-step pipeline: score, blend, reduce, plot, legend
+- Built-in reducers: PCA, NMF, ICA
+- Pluggable reducer registry
+- Static matplotlib and interactive Plotly plotting
+- Color-space legends for direct and reduction modes

multiscoresplot-1.0.6/docs/examples.md

@@ -0,0 +1,165 @@
+# Examples
+
+## Custom Reducer — UMAP
+
+Register your own dimensionality reduction method and use it like any built-in:
+
+```python
+import multiscoresplot as msp
+
+
+def umap_reducer(X, n_components, **kwargs):
+    """Reduce score matrix to RGB via UMAP.
+
+    Parameters
+    ----------
+    X : ndarray of shape (n_cells, n_gene_sets)
+        Score matrix.
+    n_components : int
+        Number of output components (always 3 for RGB).
+
+    Returns
+    -------
+    ndarray of shape (n_cells, 3)
+        Embedding with values in [0, 1].
+    """
+    import umap
+
+    embedding = umap.UMAP(n_components=n_components, **kwargs).fit_transform(X)
+    # min-max normalize each column to [0, 1]
+    for j in range(embedding.shape[1]):
+        col = embedding[:, j]
+        lo, hi = col.min(), col.max()
+        if hi > lo:
+            embedding[:, j] = (col - lo) / (hi - lo)
+    return embedding
+
+
+# Register it
+msp.register_reducer("umap", umap_reducer, component_prefix="UMAP")
+
+# Use it
+rgb = msp.reduce_to_rgb(scores, method="umap")
+msp.plot_embedding(adata, rgb, basis="umap", method="umap",
+                   gene_set_names=list(gene_sets.keys()))
+```
+
+## Different Embeddings
+
+Plot the same RGB coloring on different embeddings to compare:
+
+```python
+import matplotlib.pyplot as plt
+
+scores = msp.score_gene_sets(adata, gene_sets, inplace=True)
+rgb = msp.reduce_to_rgb(scores, method="pca")
+
+fig, axes = plt.subplots(1, 3, figsize=(18, 5))
+
+for ax, basis in zip(axes, ["umap", "pca", "X_scanorama"]):
+    msp.plot_embedding(
+        adata, rgb,
+        basis=basis,
+        method="pca",
+        gene_set_names=list(gene_sets.keys()),
+        ax=ax,
+        title=basis.upper(),
+        show=False,
+    )
+
+plt.tight_layout()
+plt.show()
+```
+
+## Comparing Reduction Methods
+
+Visualize how PCA, NMF, and ICA produce different colorings:
+
+```python
+import matplotlib.pyplot as plt
+
+scores = msp.score_gene_sets(adata, gene_sets, inplace=True)
+
+fig, axes = plt.subplots(1, 3, figsize=(18, 5))
+
+for ax, method in zip(axes, ["pca", "nmf", "ica"]):
+    rgb = msp.reduce_to_rgb(scores, method=method)
+    msp.plot_embedding(
+        adata, rgb,
+        basis="umap",
+        method=method,
+        gene_set_names=list(gene_sets.keys()),
+        ax=ax,
+        title=method.upper(),
+        show=False,
+    )
+
+plt.tight_layout()
+plt.show()
+```
+
+## Interactive Plot with Hover Metadata
+
+Explore individual cells with hover tooltips:
+
+```python
+scores = msp.score_gene_sets(adata, gene_sets, inplace=True)
+rgb = msp.reduce_to_rgb(scores, method="nmf")
+
+msp.plot_embedding_interactive(
+    adata, rgb,
+    basis="umap",
+    scores=scores,
+    method="nmf",
+    gene_set_names=list(gene_sets.keys()),
+    hover_columns=["n_counts", "cell_type"],  # any adata.obs columns
+    point_size=2,
+    width=800,
+    height=600,
+)
+```
+
+## Customizing Plot Appearance
+
+```python
+ax = msp.plot_embedding(
+    adata, rgb,
+    basis="umap",
+    method="pca",
+    gene_set_names=list(gene_sets.keys()),
+    point_size=5,
+    alpha=0.6,
+    figsize=(8, 8),
+    title="SVZ Neural Lineage",
+    legend=True,
+    legend_style="side",       # legend in a separate panel
+    legend_loc="upper right",
+    show=False,
+)
+
+# Further customize the returned axes
+ax.set_xlabel("UMAP 1", fontsize=14)
+ax.set_ylabel("UMAP 2", fontsize=14)
+```
+
+## Direct Blend for 2–3 Gene Sets
+
+When you have exactly 2 or 3 gene sets, direct blending gives the most intuitive
+color mapping:
+
+```python
+two_sets = {
+    "Stem": ["Sox2", "Pax6", "Nes"],
+    "Neuronal": ["Dcx", "Tubb3", "Neurod1"],
+}
+
+scores = msp.score_gene_sets(adata, two_sets, inplace=True)
+rgb = msp.blend_to_rgb(scores)  # blue/red by default
+
+msp.plot_embedding(
+    adata, rgb,
+    basis="umap",
+    method="direct",
+    gene_set_names=list(two_sets.keys()),
+)
+```

multiscoresplot-1.0.6/docs/getting-started.md

@@ -0,0 +1,64 @@
+# Getting Started
+
+## Installation
+
+Install from PyPI:
+
+```bash
+pip install multiscoresplot
+```
+
+For interactive Plotly plots:
+
+```bash
+pip install 'multiscoresplot[interactive]'
+```
+
+## Prerequisites
+
+multiscoresplot expects an [AnnData](https://anndata.readthedocs.io/) object with:
+
+- A precomputed dimensionality reduction embedding (e.g., UMAP, PCA, or Scanorama) stored in `adata.obsm`
+- Gene expression data (raw or normalized) accessible for scoring
+
+## Minimal Working Example
+
+```python
+import multiscoresplot as msp
+
+# 1. Define your gene sets
+gene_sets = {
+    "Stem":       ["Sox2", "Pax6", "Nes"],
+    "Neuronal":   ["Dcx", "Tubb3", "Neurod1"],
+    "Astrocytic": ["Gfap", "Aqp4", "Aldh1l1"],
+}
+
+# 2. Score gene sets per cell (stores in adata.obs as score-<name>)
+scores = msp.score_gene_sets(adata, gene_sets, inplace=True)
+
+# 3. Map scores to RGB — choose one:
+#    Blend (2–3 gene sets only)
+rgb = msp.blend_to_rgb(scores)
+#    Or reduce via dimensionality reduction (any number of gene sets)
+rgb = msp.reduce_to_rgb(scores, method="pca")
+
+# 4. Plot on a UMAP embedding (step 3 of the pipeline)
+msp.plot_embedding(
+    adata, rgb,
+    basis="umap",
+    method="pca",
+    gene_set_names=list(gene_sets.keys()),
+)
+```
+
+!!! tip "Which color mapping to use?"
+    - **`blend_to_rgb`** — Best for 2–3 gene sets. Uses intuitive multiplicative blending from white, where each gene set darkens toward its assigned color.
+    - **`reduce_to_rgb`** — Works for any number of gene sets (2+). Uses PCA, NMF, or ICA to project scores into a 3D RGB space.
+
+    See the [Pipeline Guide](pipeline.md) for a detailed comparison.
+
+## Next Steps
+
+- [Pipeline Guide](pipeline.md) — Understand each step and when to use each method
+- [API Reference](api/index.md) — Full function signatures and parameters
+- [Examples](examples.md) — Custom reducers, plot customization, and more

multiscoresplot-1.0.6/docs/index.md

@@ -0,0 +1,45 @@
+# multiscoresplot
+
+**Multi-dimensional gene set scoring and visualization for single-cell transcriptomics.**
+
+Color dimensionality reduction plots (UMAP, PCA, etc.) using a multi-dimensional
+color space derived from gene set scores — visualize the activity of multiple gene
+programs simultaneously in a single plot.
+
+## Key Features
+
+- **Score** gene sets per cell using [UCell](https://github.com/Cem-Gulec/pyUCell)
+- **Map to RGB** via multiplicative blending (2–3 sets) or dimensionality reduction (2+ sets, PCA / NMF / ICA)
+- **Plot** static matplotlib or interactive Plotly scatter plots
+- **Extend** with custom dimensionality reduction methods
+
+## Quick Example
+
+```python
+import multiscoresplot as msp
+
+# Define gene sets of interest
+gene_sets = {
+    "qNSCs": ["Id3", "Aldoc", "Slc1a3"],
+    "aNSCs": ["Egfr", "Ascl1", "Mki67"],
+    "TAP":   ["Dll1", "Dcx", "Neurod1"],
+    "NB":    ["Dcx", "Sox11", "Tubb3"],
+}
+
+# 1. Score gene sets per cell
+scores = msp.score_gene_sets(adata, gene_sets, inplace=True)
+
+# 2. Map scores to RGB colors
+rgb = msp.reduce_to_rgb(scores, method="pca")
+
+# 3. Plot
+msp.plot_embedding(
+    adata, rgb,
+    basis="umap",
+    method="pca",
+    gene_set_names=list(gene_sets.keys()),
+)
+```
+
+[Get Started](getting-started.md){ .md-button .md-button--primary }
+[API Reference](api/index.md){ .md-button }