netan 1.0.0__tar.gz

netan-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 Boris Minasenko
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

netan-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: netan
+Version: 1.0.0
+Summary: Network builder for multi-omics matrices (Rodin-compatible).
+Author: Boris Minasenko
+License: MIT
+Project-URL: Homepage, https://github.com/BM-Boris/netan-lib
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: rodin>=1.9.10
+Requires-Dist: joblib>=1.2
+Requires-Dist: tqdm>=4.65
+Dynamic: license-file
+
+# Netan — Multilayer Network Builder for Rodin‑like Objects
+
+**Netan** builds multilayer networks from omics matrices and gives you clean APIs to analyze, visualize, and export them. It supports Spearman, CLR (MI‑z), ExtraTrees‑RF, and Graphical Lasso; both *samples* and *features* node modes; stacked or multilayer graphs (with `consensus` edges); cross‑omics links; an interactive Plotly viewer; and Cytoscape‑ready CSV export.
+
+Web App: [netan.io](https://netan.io)
+
+> **Works with any *Rodin‑like* object** exposing:
+> - `r.X`: `pandas.DataFrame` (features × samples)
+> - `r.samples`: `pandas.DataFrame` (first column = sample IDs; order = `r.X.columns`)
+> - `r.features`: `pandas.DataFrame` (index = feature IDs)
+
+> - check https://github.com/BM-Boris/rodin
+
+---
+
+## Installation
+
+```bash
+pip install netan
+```
+
+> Requires Python ≥ 3.10. Dependencies (installed automatically): `rodin>=1.9.10`, `numpy`, `pandas`, `networkx`, `scikit-learn`, `joblib`, `tqdm`, `plotly`.
+
+---
+
+## Quick Start (with Rodin)
+
+Below is a **ready‑to‑run** .
+
+```python
+import rodin
+import netan
+
+# 1) Create one or multiple Rodin objects from omics data + metadata
+r1 = rodin.create( 'metabolomics.txt', 'meta.csv'
+    )
+
+r2 = rodin.create( 'transcriptomics.csv', 'meta.csv'
+    )
+
+# 2) Apply your preprocessing (Rodin handles normalization/log/scale etc.)
+r1.transform()
+r2.transform()
+
+# 3) Build a multilayer network across shared samples
+nt = netan.create([r1, r2])
+nt.build(
+    method='spearman',        # network inference method
+    edge_threshold=0.75,       # threshold on method-specific weights
+    layer_mode='multilayer',  # 'stack' or 'multilayer'
+)
+
+# 4) Interactive Plotly graph (FigureWidget)
+fig = nt.plot(
+    title='Netan: Samples × Multilayer (Spearman, threshold=0.75)',
+    node_size=12,
+    width=950,
+    height=650
+)
+
+# 5) Export an edge table compatible with Cytoscape
+nt.to_csv()
+```
+
+
+---
+
+## What Netan Does
+
+- **Aligns samples** across inputs.
+- **Infers networks** per method:
+  - `spearman`: absolute Spearman correlation, threshold ∈ [0,1].
+  - `clr`: Context Likelihood of Relatedness (MI‑based symmetric Z). Typical thresholds ~2–5.
+  - `rf`: ExtraTrees‑based symmetric importance; threshold on [0,1].
+  - `glasso`: Graphical Lasso; threshold on |partial correlation| ∈ [0,1].
+- **Combines layers**:
+  - `layer_mode='stack'`: single layer `"Entire"`.
+  - `layer_mode='multilayer'`: per‑input graphs; edges carry a `layers` set (includes `"Entire"`; adds `"consensus"` if present in all inputs).
+  - In *features*+multilayer mode: adds cross‑omics edges labeled `cross_<method>`.
+- **Layouts & communities**: assigns 2D coordinates (`x`,`y`) and lightweight component labels for easy plotting.
+- **Interactive Plotly**: legend‑driven node group toggles dynamically rebuild edge polylines; continuous color shows a colorbar.
+- **CSV export**: `source,target,weight,layer,layers` (Cytoscape‑friendly; set `List delimiter = "|"`).
+
+---
+
+### `create(rodins, names=None) -> Netan`
+Builds a `Netan` container from one or multiple Rodin‑like objects by aligning them to shared samples. Prints concise pre/post stats.
+
+- **Parameters**
+  - `rodins`: a single object or a list of objects exposing `.X` and `.samples` (optionally `.features`, `.uns`).
+  - `names`: optional list of human‑readable layer names (defaults to `r.uns['file_name']` or `layer{i}`).
+
+- **Returns**: `Netan` (with `.G` unset until you call `.build`).
+
+### `Netan.build(method='rf', node_mode='samples', layer_mode='multilayer', edge_threshold=0.025, weights=True, layout='force-directed', combine='mean', n_jobs=-1, **kwargs) -> self`
+Constructs the network in `self.G` and stores a 2D layout on nodes.
+
+- **Common parameters**
+  - `method`: `'spearman' | 'clr' | 'rf' | 'glasso'`.
+  - `node_mode`: `'samples' | 'features'` — whether nodes represent samples or features.
+  - `layer_mode`: `'stack' | 'multilayer'` — combine inputs into one layer or keep them separate with fusion.
+  - `edge_threshold`: float — threshold applied to the method‑specific weight matrix.
+  - `weights`: bool — store edge weights as `G[u][v]['weight']`.
+  - `layout`: `'force-directed'|'spring'|'circular'|'kamada_kawai'|'random'` — determines `x`,`y`.
+  - `combine`: `'mean'|'median'|'max'` — fusion rule in `samples+multilayer` mode.
+  - `n_jobs`: int — parallelism for CLR/RF.
+
+- **Method‑specific `**kwargs`**
+  - `clr`: `n_neighbors=int`.
+  - `rf`: `n_estimators=int`, `max_depth=int|None` (0/''/None ⇒ `None`).
+  - `glasso`: `alpha=float`, `max_iter=int`, `tol=float` (default 1e‑4).
+
+- **Returns**: `self`. After the call, `self.G` is a `networkx.Graph` with edge attributes `weight`, `layer`, `layers`; nodes have `x`,`y`,`display_id`,`community` (and in features mode: `object`,`file`,`type`,`compound` when metadata is available).
+
+### `Netan.plot(color=None, shape=None, layer=None, hide_isolated=False, weight_min=None, weight_max=None, node_size=10, width=None, height=None, title='Network Plot', continuous_colorscale='Viridis') -> plotly.graph_objs.FigureWidget`
+Creates an interactive Plotly network figure.
+
+- **Color/shape**
+  - *Categorical* color/shape splits nodes into legend groups; hiding a group removes its incident edges on the fly.
+  - *Continuous* color shows a colorbar (legend toggling disabled).
+
+- **Layer/weight filters**
+  - `layer`: keep an edge if that layer label is present in its `layers` set.
+  - `weight_min/max`: numeric bounds for pruning edges by weight.
+
+- **Display**: returns a `FigureWidget` suitable for notebooks/dashboards.
+
+### `Netan.to_csv(path=None, sep=',', index=False, float_format=None) -> pandas.DataFrame`
+Exports a flat edge list. Columns: `source, target, weight, layer, layers`.
+
+- In *features* node mode: adds `source_compound, target_compound` if known.
+- **Cytoscape tip**: set **Advanced → List delimiter = `|`** so `layers` parses as list.
+
+---
+
+## Threshold Tips
+
+- **Spearman**: `0.7–0.9` (use higher for sparser graphs).
+- **CLR**: `2–5` (start at `3`).
+- **RF (ExtraTrees)**: `0.02–0.10`.
+- **Glasso**: `0.1–0.3` for `edge_threshold`; increase `alpha` (`0.1–0.2`) if convergence is hard.
+
+---
+
+## Performance & Limits
+
+- Soft **density guard** around ~10,000 edges (`MAX_EDGES`); warnings suggest raising thresholds or reducing nodes.
+- Complexity:
+  - `spearman/CLR/RF`: ~O(p²) in the number of nodes per layer.
+  - `glasso`: ~O(p³)`; consider increasing `alpha` or reducing dimensionality.
+- Use `n_jobs` to parallelize CLR/RF.
+
+---
+
+## Troubleshooting
+
+- **Graph too dense** → raise `edge_threshold`, use a stricter method (`glasso`), or reduce variables.
+- **`GraphicalLasso failed`** → increase `alpha` (e.g., `0.1–0.2`), relax `tol`, ensure proper scaling.
+- **Empty plot** → check `layer` and `weight_min/max` filters and that inputs share sample IDs.
+- **Too many categories for `shape`** → map values to fewer categories (limited symbol set).
+
+---
+
+## License
+
+MIT (see `LICENSE`).
+

netan-1.0.0/README.md

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+# Netan — Multilayer Network Builder for Rodin‑like Objects
+
+**Netan** builds multilayer networks from omics matrices and gives you clean APIs to analyze, visualize, and export them. It supports Spearman, CLR (MI‑z), ExtraTrees‑RF, and Graphical Lasso; both *samples* and *features* node modes; stacked or multilayer graphs (with `consensus` edges); cross‑omics links; an interactive Plotly viewer; and Cytoscape‑ready CSV export.
+
+Web App: [netan.io](https://netan.io)
+
+> **Works with any *Rodin‑like* object** exposing:
+> - `r.X`: `pandas.DataFrame` (features × samples)
+> - `r.samples`: `pandas.DataFrame` (first column = sample IDs; order = `r.X.columns`)
+> - `r.features`: `pandas.DataFrame` (index = feature IDs)
+
+> - check https://github.com/BM-Boris/rodin
+
+---
+
+## Installation
+
+```bash
+pip install netan
+```
+
+> Requires Python ≥ 3.10. Dependencies (installed automatically): `rodin>=1.9.10`, `numpy`, `pandas`, `networkx`, `scikit-learn`, `joblib`, `tqdm`, `plotly`.
+
+---
+
+## Quick Start (with Rodin)
+
+Below is a **ready‑to‑run** .
+
+```python
+import rodin
+import netan
+
+# 1) Create one or multiple Rodin objects from omics data + metadata
+r1 = rodin.create( 'metabolomics.txt', 'meta.csv'
+    )
+
+r2 = rodin.create( 'transcriptomics.csv', 'meta.csv'
+    )
+
+# 2) Apply your preprocessing (Rodin handles normalization/log/scale etc.)
+r1.transform()
+r2.transform()
+
+# 3) Build a multilayer network across shared samples
+nt = netan.create([r1, r2])
+nt.build(
+    method='spearman',        # network inference method
+    edge_threshold=0.75,       # threshold on method-specific weights
+    layer_mode='multilayer',  # 'stack' or 'multilayer'
+)
+
+# 4) Interactive Plotly graph (FigureWidget)
+fig = nt.plot(
+    title='Netan: Samples × Multilayer (Spearman, threshold=0.75)',
+    node_size=12,
+    width=950,
+    height=650
+)
+
+# 5) Export an edge table compatible with Cytoscape
+nt.to_csv()
+```
+
+
+---
+
+## What Netan Does
+
+- **Aligns samples** across inputs.
+- **Infers networks** per method:
+  - `spearman`: absolute Spearman correlation, threshold ∈ [0,1].
+  - `clr`: Context Likelihood of Relatedness (MI‑based symmetric Z). Typical thresholds ~2–5.
+  - `rf`: ExtraTrees‑based symmetric importance; threshold on [0,1].
+  - `glasso`: Graphical Lasso; threshold on |partial correlation| ∈ [0,1].
+- **Combines layers**:
+  - `layer_mode='stack'`: single layer `"Entire"`.
+  - `layer_mode='multilayer'`: per‑input graphs; edges carry a `layers` set (includes `"Entire"`; adds `"consensus"` if present in all inputs).
+  - In *features*+multilayer mode: adds cross‑omics edges labeled `cross_<method>`.
+- **Layouts & communities**: assigns 2D coordinates (`x`,`y`) and lightweight component labels for easy plotting.
+- **Interactive Plotly**: legend‑driven node group toggles dynamically rebuild edge polylines; continuous color shows a colorbar.
+- **CSV export**: `source,target,weight,layer,layers` (Cytoscape‑friendly; set `List delimiter = "|"`).
+
+---
+
+### `create(rodins, names=None) -> Netan`
+Builds a `Netan` container from one or multiple Rodin‑like objects by aligning them to shared samples. Prints concise pre/post stats.
+
+- **Parameters**
+  - `rodins`: a single object or a list of objects exposing `.X` and `.samples` (optionally `.features`, `.uns`).
+  - `names`: optional list of human‑readable layer names (defaults to `r.uns['file_name']` or `layer{i}`).
+
+- **Returns**: `Netan` (with `.G` unset until you call `.build`).
+
+### `Netan.build(method='rf', node_mode='samples', layer_mode='multilayer', edge_threshold=0.025, weights=True, layout='force-directed', combine='mean', n_jobs=-1, **kwargs) -> self`
+Constructs the network in `self.G` and stores a 2D layout on nodes.
+
+- **Common parameters**
+  - `method`: `'spearman' | 'clr' | 'rf' | 'glasso'`.
+  - `node_mode`: `'samples' | 'features'` — whether nodes represent samples or features.
+  - `layer_mode`: `'stack' | 'multilayer'` — combine inputs into one layer or keep them separate with fusion.
+  - `edge_threshold`: float — threshold applied to the method‑specific weight matrix.
+  - `weights`: bool — store edge weights as `G[u][v]['weight']`.
+  - `layout`: `'force-directed'|'spring'|'circular'|'kamada_kawai'|'random'` — determines `x`,`y`.
+  - `combine`: `'mean'|'median'|'max'` — fusion rule in `samples+multilayer` mode.
+  - `n_jobs`: int — parallelism for CLR/RF.
+
+- **Method‑specific `**kwargs`**
+  - `clr`: `n_neighbors=int`.
+  - `rf`: `n_estimators=int`, `max_depth=int|None` (0/''/None ⇒ `None`).
+  - `glasso`: `alpha=float`, `max_iter=int`, `tol=float` (default 1e‑4).
+
+- **Returns**: `self`. After the call, `self.G` is a `networkx.Graph` with edge attributes `weight`, `layer`, `layers`; nodes have `x`,`y`,`display_id`,`community` (and in features mode: `object`,`file`,`type`,`compound` when metadata is available).
+
+### `Netan.plot(color=None, shape=None, layer=None, hide_isolated=False, weight_min=None, weight_max=None, node_size=10, width=None, height=None, title='Network Plot', continuous_colorscale='Viridis') -> plotly.graph_objs.FigureWidget`
+Creates an interactive Plotly network figure.
+
+- **Color/shape**
+  - *Categorical* color/shape splits nodes into legend groups; hiding a group removes its incident edges on the fly.
+  - *Continuous* color shows a colorbar (legend toggling disabled).
+
+- **Layer/weight filters**
+  - `layer`: keep an edge if that layer label is present in its `layers` set.
+  - `weight_min/max`: numeric bounds for pruning edges by weight.
+
+- **Display**: returns a `FigureWidget` suitable for notebooks/dashboards.
+
+### `Netan.to_csv(path=None, sep=',', index=False, float_format=None) -> pandas.DataFrame`
+Exports a flat edge list. Columns: `source, target, weight, layer, layers`.
+
+- In *features* node mode: adds `source_compound, target_compound` if known.
+- **Cytoscape tip**: set **Advanced → List delimiter = `|`** so `layers` parses as list.
+
+---
+
+## Threshold Tips
+
+- **Spearman**: `0.7–0.9` (use higher for sparser graphs).
+- **CLR**: `2–5` (start at `3`).
+- **RF (ExtraTrees)**: `0.02–0.10`.
+- **Glasso**: `0.1–0.3` for `edge_threshold`; increase `alpha` (`0.1–0.2`) if convergence is hard.
+
+---
+
+## Performance & Limits
+
+- Soft **density guard** around ~10,000 edges (`MAX_EDGES`); warnings suggest raising thresholds or reducing nodes.
+- Complexity:
+  - `spearman/CLR/RF`: ~O(p²) in the number of nodes per layer.
+  - `glasso`: ~O(p³)`; consider increasing `alpha` or reducing dimensionality.
+- Use `n_jobs` to parallelize CLR/RF.
+
+---
+
+## Troubleshooting
+
+- **Graph too dense** → raise `edge_threshold`, use a stricter method (`glasso`), or reduce variables.
+- **`GraphicalLasso failed`** → increase `alpha` (e.g., `0.1–0.2`), relax `tol`, ensure proper scaling.
+- **Empty plot** → check `layer` and `weight_min/max` filters and that inputs share sample IDs.
+- **Too many categories for `shape`** → map values to fewer categories (limited symbol set).
+
+---
+
+## License
+
+MIT (see `LICENSE`).
+

netan-1.0.0/netan/__init__.py

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+from .netan import create, Netan
+
+__all__ = ["create", "Netan"]