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Add pegasus implementations of kBET (#53)
* add global kbet metric from pegasus implementation * add per label averaged kBET implementation from pegasus * fixed label kbet naming * add new kbet components to workflow * update CHANGELOG * update documentation on running the workflow * Apply suggestions from code review Co-authored-by: Luke Zappia <[email protected]> * move changelog message to devel section * set to maximum available number of threads * Apply suggestions from code review Co-authored-by: Robrecht Cannoodt <[email protected]> * Apply suggestions from code review --------- Co-authored-by: Luke Zappia <[email protected]> Co-authored-by: Robrecht Cannoodt <[email protected]>
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‎CHANGELOG.md‎

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# task_batch_integration devel
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## New functionality
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* Added `metrics/kbet_pg` and `metrics/kbet_pg_label` components (PR #52).
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## Minor changes
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* Un-pin the scPRINT version and update parameters (PR #51)

‎CONTRIBUTING.md‎

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### Running the benchmark
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To run the benchmark, you can use the following command:
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To locally test the benchmark workflow, you can use the following command:
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```bash
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scripts/run_benchmark/run.sh
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scripts/run_benchmark/run_test_local.sh
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```
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Other scripts in `scripts/run_benchmark/` provide commands for testing on Seqera Cloud and for production runs.
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## Debugging nf-tower runs
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The actual benchmark is run on the [nf-tower platform](https://cloud.seqera.io/orgs/openproblems-bio/workspaces/openproblems-bio/watch).

‎src/metrics/kbet_pg/config.vsh.yaml‎

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__merge__: /src/api/comp_metric.yaml
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name: kbet_pg
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info:
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metric_type: embedding
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metrics:
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- name: kbet_pg
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label: kBET pegasus
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summary: kBET algorithm to determine how well batches are mixed within a cell
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type
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# TODO: transform into more readable markdown with proper formulae formatting
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description: |
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The kBET algorithm (v.0.99.6, release 4c9dafa) determines whether the label composition
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of a k nearest neighborhood of a cell is similar to the expected (global) label
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composition (Buettner et al., Nat Meth 2019). The test is repeated for a random subset
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of cells, and the results are summarized as a rejection rate over all tested
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neighborhoods.
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This implementation uses the `pegasus.calc_kBET` function.
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In Open Problems we do not run kBET on graph outputs to avoid computation-intensive
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diffusion processes being run.
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references:
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doi: 10.1038/s41592-021-01336-8
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links:
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homepage: https://pegasus.readthedocs.io/en/stable/
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documentation: https://pegasus.readthedocs.io/en/stable/api/pegasus.calc_kBET.html
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repository: https://github.com/lilab-bcb/pegasus
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min: 0
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max: 1
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maximize: true
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resources:
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- type: python_script
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path: script.py
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- path: /src/utils/read_anndata_partial.py
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engines:
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- type: docker
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image: openproblems/base_python:1.0.0
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setup:
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- type: python
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pypi:
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- pegasuspy
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- zarr<3.0
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- pandas<2.0
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- numpy<2.0
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runners:
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- type: executable
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- type: nextflow
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directives:
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label: [hightime, veryhighmem, lowcpu]

‎src/metrics/kbet_pg/script.py‎

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from tqdm import tqdm
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import sys
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import numpy as np
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import anndata as ad
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import pegasus as pg
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import pegasusio
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from scipy.sparse import csr_matrix
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def compute_kbet(mmdata, *args, **kwargs):
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stat_mean, pvalue_mean, accept_rate = pg.calc_kBET(mmdata, *args, **kwargs)
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return accept_rate
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## VIASH START
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par = {
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'input_integrated': 'resources_test/task_batch_integration/cxg_immune_cell_atlas/integrated_full.h5ad',
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'output': 'output.h5ad',
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}
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meta = {
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'name': 'kbet_pg',
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}
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## VIASH END
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sys.path.append(meta["resources_dir"])
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from read_anndata_partial import read_anndata
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n_threads = meta["cpus"] or -1
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print('Read input...', flush=True)
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adata = read_anndata(par['input_integrated'], obs='obs', obsm='obsm', uns='uns')
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adata.obs = read_anndata(par['input_solution'], obs='obs').obs
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adata.uns |= read_anndata(par['input_solution'], uns='uns').uns
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print(adata, flush=True)
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print('Convert to pegasusio.MultimodalData...', flush=True)
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adata.X = csr_matrix(adata.shape)
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mmdata = pegasusio.MultimodalData(adata)
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print('Compute global kBET...', flush=True)
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score = compute_kbet(
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mmdata,
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attr="batch",
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rep="emb",
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K=50,
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n_jobs=n_threads,
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)
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print('Global kBET score:', score, flush=True)
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print('Create output AnnData object', flush=True)
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metric_name = meta['name']
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output = ad.AnnData(
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uns={
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'dataset_id': adata.uns['dataset_id'],
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'normalization_id': adata.uns['normalization_id'],
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'method_id': adata.uns['method_id'],
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'metric_ids': [ metric_name ],
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'metric_values': [ score ]
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}
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)
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print('Write data to file', flush=True)
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output.write_h5ad(par['output'], compression='gzip')

‎src/metrics/kbet_pg_label/config.vsh.yaml‎

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__merge__: /src/api/comp_metric.yaml
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name: kbet_pg_label
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info:
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metric_type: embedding
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metrics:
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- name: kbet_pg_label
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label: kBET pegasus label
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summary: kBET algorithm to determine how well batches are mixed within a cell
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type
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description: |
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The kBET algorithm (v.0.99.6, release 4c9dafa) determines whether the label composition
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of a k nearest neighborhood of a cell is similar to the expected (global) label
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composition (Buettner et al., Nat Meth 2019). The test is repeated for a random subset
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of cells, and the results are summarized as a rejection rate over all tested
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neighborhoods.
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This implementation uses the `pegasus.calc_kBET` function per cell type and the rejection
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rate is averaged over all cell types.
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In Open Problems we do not run kBET on graph outputs to avoid computation-intensive
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diffusion processes being run.
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references:
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doi: 10.1038/s41592-021-01336-8
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links:
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homepage: https://pegasus.readthedocs.io/en/stable/
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documentation: https://pegasus.readthedocs.io/en/stable/api/pegasus.calc_kBET.html
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repository: https://github.com/lilab-bcb/pegasus
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min: 0
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max: 1
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maximize: true
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resources:
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- type: python_script
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path: script.py
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- path: /src/utils/read_anndata_partial.py
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engines:
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- type: docker
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image: openproblems/base_python:1.0.0
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setup:
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- type: python
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pypi:
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- pegasuspy
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- zarr<3.0
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- pandas<2.0
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- numpy<2.0
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runners:
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- type: executable
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- type: nextflow
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directives:
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label: [hightime, veryhighmem, lowcpu]

‎src/metrics/kbet_pg_label/script.py‎

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from tqdm import tqdm
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import sys
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import numpy as np
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import anndata as ad
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import pegasus as pg
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import pegasusio
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from scipy.sparse import csr_matrix
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from joblib import Parallel, delayed
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def compute_kbet(mmdata, *args, **kwargs):
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stat_mean, pvalue_mean, accept_rate = pg.calc_kBET(mmdata, *args, **kwargs)
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return accept_rate
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## VIASH START
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par = {
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'input_integrated': 'resources_test/task_batch_integration/cxg_immune_cell_atlas/integrated_full.h5ad',
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'output': 'output.h5ad',
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}
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meta = {
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'name': 'foo',
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}
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## VIASH END
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sys.path.append(meta["resources_dir"])
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from read_anndata_partial import read_anndata
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n_threads = meta["cpus"] or -1
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print('Read input...', flush=True)
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adata = read_anndata(par['input_integrated'], obs='obs', obsm='obsm', uns='uns')
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adata.obs = read_anndata(par['input_solution'], obs='obs').obs
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adata.uns |= read_anndata(par['input_solution'], uns='uns').uns
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adata.X = csr_matrix(adata.shape)
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print(adata, flush=True)
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print('Compute cell type averaged kBET...', flush=True)
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cell_types = adata.obs['cell_type'].unique()
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scores = []
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mmdata_per_cell_type = []
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# collect all adata subsets
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for cell_type in cell_types:
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ad_sub = adata[adata.obs['cell_type'] == cell_type]
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if ad_sub.obs['batch'].nunique() <= 1:
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print(f'Skipping cell type {cell_type} because it\'s present in only one batch', flush=True)
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continue
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_mmdata = pegasusio.MultimodalData(ad_sub.copy())
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mmdata_per_cell_type.append(_mmdata)
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# compute kBET scores
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scores = Parallel(n_jobs=n_threads)(
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delayed(compute_kbet)(
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_mmdata,
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attr="batch",
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rep="emb",
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K=50,
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use_cache=False,
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n_jobs=1,
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) for _mmdata in tqdm(
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mmdata_per_cell_type,
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desc=f'Compute per cell type with {n_threads} threads',
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miniters=1,
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)
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)
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score = np.nanmean(scores)
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print('Cell type averaged kBET score:', score, flush=True)
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print('Create output AnnData object', flush=True)
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metric_name = meta['name']
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output = ad.AnnData(
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uns={
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'dataset_id': adata.uns['dataset_id'],
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'normalization_id': adata.uns['normalization_id'],
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'method_id': adata.uns['method_id'],
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'metric_ids': [ metric_name ],
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'metric_values': [ score ]
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}
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)
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print('Write data to file', flush=True)
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output.write_h5ad(par['output'], compression='gzip')

‎src/workflows/run_benchmark/config.vsh.yaml‎

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- name: metrics/isolated_label_asw
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- name: metrics/isolated_label_f1
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- name: metrics/kbet
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- name: metrics/kbet_pg
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- name: metrics/kbet_pg_label
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- name: metrics/lisi
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- name: metrics/pcr
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# data processors

‎src/workflows/run_benchmark/main.nf‎

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isolated_label_asw,
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isolated_label_f1,
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kbet,
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kbet_pg,
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kbet_pg_label,
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lisi,
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pcr
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]

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