multiscoresplot 1.0.5__tar.gz → 2.0.0__tar.gz

{multiscoresplot-1.0.5 → multiscoresplot-2.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: multiscoresplot
-Version: 1.0.5
+Version: 2.0.0
 Summary: Multi-dimensional gene set scoring and visualization for single-cell transcriptomics
 Project-URL: Homepage, https://github.com/AndreMacedo88/multiscoresplot
 Project-URL: Documentation, https://AndreMacedo88.github.io/multiscoresplot/
@@ -71,21 +71,16 @@ gene_sets = {
 # 1. Score gene sets per cell
 scores = msp.score_gene_sets(adata, gene_sets, inplace=True)
 
-# 2. Map scores to RGB colors
+# 2. Map scores to RGB colors (returns RGBResult with metadata)
 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()),
-)
+# 3. Plot — method & gene_set_names auto-detected from RGBResult
+msp.plot_embedding(adata, rgb, basis="X_umap")
 ```
 
 ## Pipeline
 
-multiscoresplot follows a 5-step pipeline:
+multiscoresplot follows a 3-step pipeline:
 
 ### Step 1 — Score gene sets
 
@@ -104,9 +99,11 @@ scores = msp.score_gene_sets(
 )
 ```
 
-### Step 2 — Blend to RGB (2–3 gene sets)
+### Step 2 — Map scores to RGB
+
+Convert gene set scores into per-cell RGB colors. Both functions return an `RGBResult` that carries the RGB array plus metadata (method, gene set names, colors) used automatically by the plotting functions.
 
-For 2–3 gene sets, use multiplicative blending from white. Each gene set darkens toward its base color proportional to the score.
+**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)
@@ -116,9 +113,7 @@ 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
@@ -126,59 +121,51 @@ 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.
 
 ```python
-# Static matplotlib plot
-msp.plot_embedding(
-    adata, rgb,
-    basis="umap",
-    method="pca",
-    gene_set_names=["qNSCs", "aNSCs", "TAP", "NB"],
-)
+# Static matplotlib plot — method & gene_set_names auto-detected from RGBResult
+msp.plot_embedding(adata, rgb, basis="X_umap")
 
 # Options
 ax = msp.plot_embedding(
     adata, rgb,
-    basis="umap",
-    method="pca",
-    gene_set_names=["qNSCs", "aNSCs", "TAP", "NB"],
+    basis="X_umap",
     legend=True,              # show color legend (default)
     legend_style="inset",     # "inset" or "side"
     legend_loc="lower right", # legend position
+    legend_size=0.30,         # legend size (fraction of plot)
+    legend_resolution=128,    # legend image resolution
     point_size=3,
     alpha=0.8,
     figsize=(6, 6),
+    dpi=100,                  # figure resolution
     title="SVZ lineage",
     show=False,               # return axes instead of displaying
 )
 ```
 
-### 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(
     adata, rgb,
-    basis="umap",
+    basis="X_umap",
     scores=scores,
-    method="nmf",
-    gene_set_names=["qNSCs", "aNSCs", "TAP", "NB"],
-    hover_columns=["n_counts", "cell_type"],  # extra adata.obs columns
+    hover_columns=["n_counts", "cell_type", "Dcx"],  # obs columns or gene names
     legend=True,
     legend_loc="lower right",
     point_size=2,
-    width=600,
-    height=500,
+    figsize=(6.5, 6.0),      # figure size in inches
+    dpi=100,                  # pixels = figsize * dpi
 )
 ```
 
-### 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
@@ -216,18 +203,28 @@ 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                               |
-| --------------------------------------------------- | ----------------------------------------- |
-| `score_gene_sets(adata, gene_sets)`                 | Score gene sets per cell via pyUCell      |
-| `blend_to_rgb(scores)`                              | Multiplicative blend to RGB (2–3 sets)    |
-| `reduce_to_rgb(scores, method="pca")`               | Dimensionality reduction to RGB (2+ sets) |
-| `plot_embedding(adata, rgb, basis=...)`             | Static matplotlib scatter plot            |
-| `plot_embedding_interactive(adata, rgb, basis=...)` | Interactive Plotly scatter plot           |
-| `render_legend(ax, method)`                         | Draw color-space legend on axes           |
-| `register_reducer(name, fn)`                        | Register a custom reduction method        |
-| `get_component_labels(method)`                      | Get axis labels for a reduction method    |
+| Function / Class                                    | Description                                         |
+| --------------------------------------------------- | --------------------------------------------------- |
+| `score_gene_sets(adata, gene_sets)`                 | Score gene sets per cell via pyUCell                |
+| `blend_to_rgb(scores)`                              | Multiplicative blend to RGB (2–3 sets) → RGBResult  |
+| `reduce_to_rgb(scores, method="pca")`               | Dimensionality reduction to RGB (2+ sets) → RGBResult |
+| `RGBResult`                                         | RGB array + metadata (method, gene set names, colors) |
+| `plot_embedding(adata, rgb, basis=...)`             | Static matplotlib scatter plot                      |
+| `plot_embedding_interactive(adata, rgb, basis=...)` | Interactive Plotly scatter plot                     |
+| `render_legend(ax, method)`                         | Draw color-space legend on axes                     |
+| `register_reducer(name, fn)`                        | Register a custom reduction method                  |
+| `get_component_labels(method)`                      | Get axis labels for a reduction method              |
 
 ## Development
 

{multiscoresplot-1.0.5 → multiscoresplot-2.0.0}/README.md

@@ -38,21 +38,16 @@ gene_sets = {
 # 1. Score gene sets per cell
 scores = msp.score_gene_sets(adata, gene_sets, inplace=True)
 
-# 2. Map scores to RGB colors
+# 2. Map scores to RGB colors (returns RGBResult with metadata)
 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()),
-)
+# 3. Plot — method & gene_set_names auto-detected from RGBResult
+msp.plot_embedding(adata, rgb, basis="X_umap")
 ```
 
 ## Pipeline
 
-multiscoresplot follows a 5-step pipeline:
+multiscoresplot follows a 3-step pipeline:
 
 ### Step 1 — Score gene sets
 
@@ -71,9 +66,11 @@ scores = msp.score_gene_sets(
 )
 ```
 
-### Step 2 — Blend to RGB (2–3 gene sets)
+### Step 2 — Map scores to RGB
+
+Convert gene set scores into per-cell RGB colors. Both functions return an `RGBResult` that carries the RGB array plus metadata (method, gene set names, colors) used automatically by the plotting functions.
 
-For 2–3 gene sets, use multiplicative blending from white. Each gene set darkens toward its base color proportional to the score.
+**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)
@@ -83,9 +80,7 @@ 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
@@ -93,59 +88,51 @@ 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.
 
 ```python
-# Static matplotlib plot
-msp.plot_embedding(
-    adata, rgb,
-    basis="umap",
-    method="pca",
-    gene_set_names=["qNSCs", "aNSCs", "TAP", "NB"],
-)
+# Static matplotlib plot — method & gene_set_names auto-detected from RGBResult
+msp.plot_embedding(adata, rgb, basis="X_umap")
 
 # Options
 ax = msp.plot_embedding(
     adata, rgb,
-    basis="umap",
-    method="pca",
-    gene_set_names=["qNSCs", "aNSCs", "TAP", "NB"],
+    basis="X_umap",
     legend=True,              # show color legend (default)
     legend_style="inset",     # "inset" or "side"
     legend_loc="lower right", # legend position
+    legend_size=0.30,         # legend size (fraction of plot)
+    legend_resolution=128,    # legend image resolution
     point_size=3,
     alpha=0.8,
     figsize=(6, 6),
+    dpi=100,                  # figure resolution
     title="SVZ lineage",
     show=False,               # return axes instead of displaying
 )
 ```
 
-### 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(
     adata, rgb,
-    basis="umap",
+    basis="X_umap",
     scores=scores,
-    method="nmf",
-    gene_set_names=["qNSCs", "aNSCs", "TAP", "NB"],
-    hover_columns=["n_counts", "cell_type"],  # extra adata.obs columns
+    hover_columns=["n_counts", "cell_type", "Dcx"],  # obs columns or gene names
     legend=True,
     legend_loc="lower right",
     point_size=2,
-    width=600,
-    height=500,
+    figsize=(6.5, 6.0),      # figure size in inches
+    dpi=100,                  # pixels = figsize * dpi
 )
 ```
 
-### 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
@@ -183,18 +170,28 @@ 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                               |
-| --------------------------------------------------- | ----------------------------------------- |
-| `score_gene_sets(adata, gene_sets)`                 | Score gene sets per cell via pyUCell      |
-| `blend_to_rgb(scores)`                              | Multiplicative blend to RGB (2–3 sets)    |
-| `reduce_to_rgb(scores, method="pca")`               | Dimensionality reduction to RGB (2+ sets) |
-| `plot_embedding(adata, rgb, basis=...)`             | Static matplotlib scatter plot            |
-| `plot_embedding_interactive(adata, rgb, basis=...)` | Interactive Plotly scatter plot           |
-| `render_legend(ax, method)`                         | Draw color-space legend on axes           |
-| `register_reducer(name, fn)`                        | Register a custom reduction method        |
-| `get_component_labels(method)`                      | Get axis labels for a reduction method    |
+| Function / Class                                    | Description                                         |
+| --------------------------------------------------- | --------------------------------------------------- |
+| `score_gene_sets(adata, gene_sets)`                 | Score gene sets per cell via pyUCell                |
+| `blend_to_rgb(scores)`                              | Multiplicative blend to RGB (2–3 sets) → RGBResult  |
+| `reduce_to_rgb(scores, method="pca")`               | Dimensionality reduction to RGB (2+ sets) → RGBResult |
+| `RGBResult`                                         | RGB array + metadata (method, gene set names, colors) |
+| `plot_embedding(adata, rgb, basis=...)`             | Static matplotlib scatter plot                      |
+| `plot_embedding_interactive(adata, rgb, basis=...)` | Interactive Plotly scatter plot                     |
+| `render_legend(ax, method)`                         | Draw color-space legend on axes                     |
+| `register_reducer(name, fn)`                        | Register a custom reduction method                  |
+| `get_component_labels(method)`                      | Get axis labels for a reduction method              |
 
 ## Development
 

{multiscoresplot-1.0.5 → multiscoresplot-2.0.0}/docs/api/colorspace.md

@@ -2,6 +2,16 @@
 
 Color mapping from gene set scores to RGB (pipeline steps 2–3).
 
+Both `blend_to_rgb` and `reduce_to_rgb` return an `RGBResult` object that wraps
+the RGB array with metadata (method, gene set names, colors). This metadata is
+auto-detected by the plotting functions.
+
+## RGBResult
+
+::: multiscoresplot.RGBResult
+
+---
+
 ## Blending (2–3 gene sets)
 
 ::: multiscoresplot.blend_to_rgb

{multiscoresplot-1.0.5 → multiscoresplot-2.0.0}/docs/api/index.md

@@ -2,14 +2,15 @@
 
 ## Overview
 
-| Function | Description | Pipeline Step |
-|----------|-------------|---------------|
+| Function / Class | 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 3 |
-| [`plot_embedding`](plotting.md) | Static matplotlib scatter plot | Step 4 |
-| [`plot_embedding_interactive`](interactive.md) | Interactive Plotly scatter plot | Step 4b |
-| [`render_legend`](legend.md) | Draw color-space legend on axes | Step 5 |
+| [`reduce_to_rgb`](colorspace.md#multiscoresplot.reduce_to_rgb) | Dimensionality reduction to RGB (2+ sets) | Step 2 |
+| [`RGBResult`](colorspace.md#multiscoresplot.RGBResult) | Return type of `blend_to_rgb` / `reduce_to_rgb` with metadata | 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 |
 

multiscoresplot-2.0.0/docs/changelog.md

@@ -0,0 +1,35 @@
+# Changelog
+
+## 2.0.0
+
+### Breaking changes
+- `blend_to_rgb` and `reduce_to_rgb` now return `RGBResult` (carries RGB array + metadata). The object supports numpy array protocol, so `np.asarray(result)`, indexing, and comparisons still work.
+- `plot_embedding` and `plot_embedding_interactive`: `basis=` now takes the **full obsm key** (e.g. `"X_umap"`, `"umap_consensus"`). The old short form (`basis="umap"`) still works but emits a `DeprecationWarning`.
+- `plot_embedding`: `legend=True` (default) now **requires** a known method. Previously it silently skipped the legend when `method=None`; now it raises `ValueError`. Pass `legend=False` or provide `method=`, or use an `RGBResult`.
+- `plot_embedding_interactive`: `width`/`height` replaced by `figsize` (inches) + `dpi`. Pixel dimensions = `figsize * dpi`.
+
+### New features
+- **`RGBResult`**: new dataclass returned by `blend_to_rgb` / `reduce_to_rgb`. Carries `method`, `gene_set_names`, and `colors` metadata that plotting functions auto-detect.
+- **`plot_embedding`**: new params `legend_size`, `legend_resolution`, `dpi`.
+- **`plot_embedding_interactive`**: new param `legend_kwargs`. `figsize`/`dpi` replace `width`/`height`.
+- **Both plotting functions**: consistent `legend_size`, `legend_resolution`, and `legend_kwargs` params.
+- **`hover_columns`** now falls back to `adata.var_names` for gene expression values (sparse matrices supported).
+- **`gene_set_names`** behavior is now consistent between static and interactive plots.
+
+## 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-1.0.5 → multiscoresplot-2.0.0}/docs/examples.md

@@ -38,10 +38,9 @@ def umap_reducer(X, n_components, **kwargs):
 # Register it
 msp.register_reducer("umap", umap_reducer, component_prefix="UMAP")
 
-# Use it
+# Use it — method auto-detected from RGBResult
 rgb = msp.reduce_to_rgb(scores, method="umap")
-msp.plot_embedding(adata, rgb, basis="umap", method="umap",
-                   gene_set_names=list(gene_sets.keys()))
+msp.plot_embedding(adata, rgb, basis="X_umap")
 ```
 
 ## Different Embeddings
@@ -56,12 +55,10 @@ 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"]):
+for ax, basis in zip(axes, ["X_umap", "X_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,
@@ -86,9 +83,7 @@ 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()),
+        basis="X_umap",
         ax=ax,
         title=method.upper(),
         show=False,
@@ -108,14 +103,12 @@ rgb = msp.reduce_to_rgb(scores, method="nmf")
 
 msp.plot_embedding_interactive(
     adata, rgb,
-    basis="umap",
+    basis="X_umap",
     scores=scores,
-    method="nmf",
-    gene_set_names=list(gene_sets.keys()),
-    hover_columns=["n_counts", "cell_type"],  # any adata.obs columns
+    hover_columns=["n_counts", "cell_type", "Dcx"],  # obs columns or gene names
     point_size=2,
-    width=800,
-    height=600,
+    figsize=(8.0, 6.0),
+    dpi=100,
 )
 ```
 
@@ -124,16 +117,16 @@ msp.plot_embedding_interactive(
 ```python
 ax = msp.plot_embedding(
     adata, rgb,
-    basis="umap",
-    method="pca",
-    gene_set_names=list(gene_sets.keys()),
+    basis="X_umap",
     point_size=5,
     alpha=0.6,
     figsize=(8, 8),
+    dpi=150,
     title="SVZ Neural Lineage",
     legend=True,
     legend_style="side",       # legend in a separate panel
     legend_loc="upper right",
+    legend_size=0.35,          # legend size (fraction of plot)
     show=False,
 )
 
@@ -156,10 +149,6 @@ two_sets = {
 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()),
-)
+# method="direct" and gene_set_names auto-detected from RGBResult
+msp.plot_embedding(adata, rgb, basis="X_umap")
 ```

{multiscoresplot-1.0.5 → multiscoresplot-2.0.0}/docs/getting-started.md

@@ -37,18 +37,13 @@ gene_sets = {
 scores = msp.score_gene_sets(adata, gene_sets, inplace=True)
 
 # 3. Map scores to RGB — choose one:
-#    Direct blend (2–3 gene sets only)
+#    Blend (2–3 gene sets only)
 rgb = msp.blend_to_rgb(scores)
-#    Or dimensionality reduction (any number of gene sets)
+#    Or reduce via dimensionality reduction (any number of gene sets)
 rgb = msp.reduce_to_rgb(scores, method="pca")
 
-# 4. Plot on a UMAP embedding
-msp.plot_embedding(
-    adata, rgb,
-    basis="umap",
-    method="pca",
-    gene_set_names=list(gene_sets.keys()),
-)
+# 4. Plot on a UMAP embedding — method & labels auto-detected from RGBResult
+msp.plot_embedding(adata, rgb, basis="X_umap")
 ```
 
 !!! tip "Which color mapping to use?"

{multiscoresplot-1.0.5 → multiscoresplot-2.0.0}/docs/index.md

@@ -9,8 +9,7 @@ programs simultaneously in a single plot.
 ## Key Features
 
 - **Score** gene sets per cell using [UCell](https://github.com/Cem-Gulec/pyUCell)
-- **Blend** 2–3 gene sets to RGB via multiplicative blending
-- **Reduce** any number of gene sets to RGB via PCA / NMF / ICA
+- **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
 
@@ -30,16 +29,11 @@ gene_sets = {
 # 1. Score gene sets per cell
 scores = msp.score_gene_sets(adata, gene_sets, inplace=True)
 
-# 2. Map scores to RGB colors
+# 2. Map scores to RGB colors (returns RGBResult with metadata)
 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()),
-)
+# 3. Plot — method & gene_set_names auto-detected from RGBResult
+msp.plot_embedding(adata, rgb, basis="X_umap")
 ```
 
 [Get Started](getting-started.md){ .md-button .md-button--primary }