sc-robust 0.1.7

A statistically robust pipeline for building cell-cell graphs from single cell RNAseq

sc_robust

A pipeline for robust reproducible single cell processing

Installation

Option 1: pip (CPU-only FAISS)

python -m venv .venv && source .venv/bin/activate  # optional
pip install -r requirements.txt

Notes:

• The requirements pin faiss-cpu. On some platforms, pip wheels may be limited. If pip fails on FAISS, use Conda below.
• GPU FAISS is not required for this package; CPU FAISS works well for typical sizes.

Option 2: Conda (recommended for FAISS/igraph)

conda create -n sc_robust python=3.10 -y
conda activate sc_robust
conda install -c conda-forge anndata numpy scipy matplotlib seaborn statsmodels networkx igraph leidenalg pymetis -y
conda install -c pytorch faiss-cpu -y   # or: conda install -c conda-forge faiss
pip install torch count_split anticor_features

Optional/adjacent tools

• scanpy: plotting / clustering convenience (not required by sc_robust core)
• umap-learn: if you want to run UMAP on precomputed graphs

Python compatibility

• Tested on Python 3.10+. Other versions may work, but 3.10 is recommended.

Data conventions

• Count matrices are cells×genes (rows = cells, columns = genes).
• Graph adjacencies are cells×cells.
• Embeddings/PCs are n_cells×n_dims.
• anticor_features expects cells in columns (genes×cells); sc_robust handles the transpose internally.

QC Workflow Example

The repository ships a reference quality-control scaffold in sc_robust/qc.py. It computes mitochondrial / ribosomal / lncRNA metrics, derives heuristic thresholds, and groups cells into interpretable QC buckets. A minimal example:

from pathlib import Path
import anndata as ad
from sc_robust.qc import quantify_qc_metrics, determine_qc_thresholds, classify_qc_categories

adata = ad.read_h5ad("data/anndata.h5ad")

# Phase 1 – quantify QC metrics (optionally emits plots)
quant_res = quantify_qc_metrics(
    adata,
    plotting_dir=Path("figures/qc"),
    make_plots=True,
    plot_annotation_keys=("sample",),  # columns from `adata.obs` to color plots
)

# Merge the QC metrics back into the working AnnData
qc_df = quant_res.to_dataframe(prefix="qc_")
adata.obs = adata.obs.join(qc_df, how="left")

# Phase 2 – derive thresholds and classify cells
thresholds = determine_qc_thresholds(quant_res.adata)
summary = classify_qc_categories(quant_res.adata, thresholds)

# Filter to high-quality cells
filtered = quant_res.adata[quant_res.adata.obs["qc_keep"].to_numpy()].copy()
print(summary)
print(filtered)

See sc_robust/qc.py for a ready-to-run perform_qc_and_filtering orchestration function that combines these steps and materializes plots.

Single-Graph Usage (No Splits)

You can reuse the graph-building pipeline on any embedding or feature matrix and cluster with Leiden without using train/validation splits.

Example:

import numpy as np
from sc_robust.utils import build_single_graph, single_graph_and_leiden

# Suppose E is an (n_samples, n_dims) embedding
E = np.random.randn(500, 32).astype(np.float32)

# Build a graph using cosine metric (default)
G = build_single_graph(E, k=None, metric='cosine', symmetrize='none')

# Or build and cluster in one step
G, labels = single_graph_and_leiden(E, k=None, metric='cosine', resolution=1.0)

# To use Euclidean distance instead of cosine
G_l2 = build_single_graph(E, k=None, metric='l2', symmetrize='max')

Notes:

• The default k is round(log(n)) floored to 10, capped by 200 and by n (and requires n >= 3*k).
• Weighting uses the package’s per-node linear rescale; masking is adaptive per-node by distance differences.
• Metrics:
  • cosine (default): inner product on L2-normalized rows.
  • l2: squared Euclidean distances via FAISS IndexFlatL2.
  • ip: raw inner product (pseudo-distance -sim).

Robust Pipeline Tutorial

This is the split-based workflow that builds a consensus KNN graph from train/val splits, then clusters with Leiden.

Basics

Gene Modules (Single Dataset + Cohort Meta-Analysis)

sc_robust can reuse the spearman.hdf5 artifacts written by anticor_features (via robust(..., scratch_dir=...)) to build gene–gene graphs, discover positive co-regulated gene modules, and summarize negative antagonism between those modules.

Key idea:

• Positive correlations answer: “same cell-state program” → used for module discovery (Leiden).
• Negative correlations answer: “mutually exclusive programs” → used only for module antagonism summaries.

Single dataset (one scratch dir)

from sc_robust.sc_robust import robust

ro = robust(
    adata,
    gene_ids=adata.var["gene_ids"].tolist(),
    scratch_dir="results/sample_001",
    offline_mode=True,
)

# Optional post-step (writes artifacts under scratch_dir and records paths in ro.provenance on save)
ro.run_gene_modules(split_mode="union", resolution=1.0)
ro.save("results/sample_001/robust_object.dill")

Outputs under scratch_dir:

• gene_modules.tsv.gz
• gene_edges_pos.tsv.gz, gene_edges_neg.tsv.gz
• gene_module_antagonism.tsv.gz
• module_stats.json
• gene_modules.report.json

Cohort meta-analysis (many scratch dirs)

from pathlib import Path
from sc_robust.gene_modules import run_gene_module_meta_analysis_for_cohort

scratch_dirs = [Path("results") / s for s in ["S1", "S2", "S3"]]
out = run_gene_module_meta_analysis_for_cohort(
    scratch_dirs,
    out_dir=Path("results") / "gene_module_meta",
)
print(out["replicated_modules"])  # replicated_modules.tsv.gz (annotated with support_n_samples)

Outputs under out_dir:

• gene_modules_manifest.tsv.gz
• replicated_modules.tsv.gz (includes support_n_samples)
• replicated_module_instances.tsv.gz
• replicated_module_antagonism.tsv.gz
• *.report.json sidecars (quick summary + artifact pointers)

import anndata as ad
import scanpy as sc
from sc_robust import robust
from sc_robust.utils import perform_leiden_clustering

# Load your AnnData
adata = ad.read_h5ad("path/to/data.h5ad")

# Optional: ensure gene identifiers are accessible
gene_ids = (
    adata.var.get("gene_ids", adata.var.get("gene_name", adata.var.index)).tolist()
)

# Build the robust object (splits -> normalize -> feature select -> PCs -> graph)
ro = robust(
    adata,
    gene_ids=gene_ids,
    norm_function="pf_log",
    # anticor_features integration knobs
    scratch_dir="scratch/anticor",
    offline_mode=True,  # hard-enforce no live GO/g:Profiler lookups
    use_live_pathway_lookup=False,
    do_plot=False,
)

# The consensus graph is available as a scipy.sparse COO matrix
G = ro.graph

# Cluster with Leiden (igraph/leidenalg backend) or Scanpy
clusters, partition, labels = perform_leiden_clustering(G, resolution_parameter=1.0)
adata.obs["leiden"] = labels.astype(int).astype("category")

# Or use Scanpy if preferred
# sc.tl.leiden(adata, adjacency=G.tocsr())

Pseudobulk Preparation (Optional)

from sc_robust.process_de_test_split import prep_sample_pseudobulk

# Build METIS-based pseudobulk partitions from the graph and counts
pb_exprs, pb_meta = prep_sample_pseudobulk(
    ro.graph,                 # COO weighted adjacency
    ro.test_counts,           # counts matrix (cells x genes)
    cells_per_pb=10,          # target group size
    sample_vect=adata.obs['sample'].tolist(),
    cluster_vect=adata.obs['leiden'].tolist(),
    gene_ids=adata.var_names.tolist(),
    coords=adata.obsm.get('X_umap'),
    cell_meta=adata.obs,      # optional cell-level covariates for aggregation
)

Tips

• The default neighbor count is adaptive: k ≈ round(log(n)) but capped and masked locally.
• The robust object exposes: train/val/test (normalized), train_pcs/val_pcs, selected features, and the final graph.
• If no reproducible structure is found during PC validation, ro.no_reproducible_pcs=True and ro.graph=None (this is expected on null/no-structure data).

Offline note

• With recent anticor_features, pathway-based pre-removal uses shipped ID banks by default (no network) unless use_live_pathway_lookup=True or the bank is missing for your species.
• If no ID bank is available for your species (or you request custom pathway lists), anticor_features may require live lookup unless you provide id_bank_dir=....
• If you need a guarantee that no live lookup can happen, pass offline_mode=True (recommended for HPC/sandboxed environments). When a live lookup would otherwise be required, sc_robust will now raise a single actionable error with fixes (disable live lookup, provide an ID bank, or skip pathway removal).

HPC/offline recommended defaults

• Use 3-way splits (train/val/test). If you pass 2-way splits, sc_robust will copy val into test and emit a warning: you must not use test for downstream DE in that case (double dipping).
• Consider setting:
  • offline_mode=True (hard guarantee: no network)
  • use_live_pathway_lookup=False (explicitly opt out of live GO/g:Profiler)
  • scratch_dir=... to persist anticor_features artifacts and kept-feature manifests per split (ordering + pathway-removal provenance when available)
  • pre_remove_pathways=[] if you want to skip pathway-based pre-removal entirely
  • count_split_quiet=True to suppress noisy stdout from count_split (set False to see its progress prints)
  • count_split_bin_size=... if you need to tune memory/performance during splitting
• Graph construction requires n_cells >= 3*k_used (with defaults, effectively n_cells >= 30), and the returned adjacency is always n_cells×n_cells in shape.

API Reference

• sc_robust.robust(...)

  • Builds a consensus KNN graph from train/val splits. Key knobs: scratch_dir, offline_mode, use_live_pathway_lookup, pre_remove_pathways, count_split_bin_size, count_split_quiet. Attributes: graph (COO adjacency), indices/distances/weights (per-node lists), train/val/test, train_pcs/val_pcs, train_feature_df/val_feature_df.

• sc_robust.utils.perform_leiden_clustering(coo_mat, resolution_parameter=1.0)

  • Converts COO to igraph and runs Leiden. Returns (clusters_list, partition_obj, labels_array).

• sc_robust.utils.build_single_graph(embedding_or_X, k=None, metric='cosine', min_k=None, symmetrize='none', use_gpu=False)

  • Builds a weighted KNN graph directly from an embedding or features using existing masking/weighting. Returns a COO adjacency.

• sc_robust.utils.single_graph_and_leiden(embedding_or_X, k=None, metric='cosine', resolution=1.0, symmetrize='none', use_gpu=False)

  • Convenience: builds a graph and runs Leiden. Returns (graph_coo, labels_array).

• sc_robust.process_de_test_split.prep_sample_pseudobulk(in_graph, X, cells_per_pb=10, sample_vect=None, cluster_vect=None, gene_ids=None, coords=None, cell_meta=None)

  • METIS partitions of cells into pseudobulk groups based on the graph, with expression and metadata aggregation. Returns (pb_exprs, annotation_df).

• sc_robust.find_consensus.tsvd(temp_mat, npcs=250)

  • TruncatedSVD (samples x features) → embedding (n_samples, npcs).

• sc_robust.find_consensus.find_one_graph(pcs, k=None, metric='cosine', use_gpu=False)

  • Row-wise KNN neighbors and local-difference mask. Returns (indices, distances, mask) (torch tensors).

• sc_robust.find_consensus.process_idx_dist_mask_to_g(indexes, distances, local_mask)

  • Converts per-node neighbors, distances, and mask into a weighted COO adjacency using the package’s linear weighting.

Differential Expression Updates

• The differential-expression helpers automatically merge the packaged ensg_annotations_abbreviated.txt lookup so downstream tables always surface gene_id and gene_name columns, even when the caller does not supply annotations.
• Pathway enrichment now hashes gene memberships and, when n_jobs != 1, uses a process-backed executor by default to sidestep the Python GIL. Environments that block process creation will emit a warning and transparently fall back to threaded execution; you can also force threading with backend="thread".