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fix error in control methods #107

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Merged
ghar1821 merged 2 commits into from
Oct 1, 2025
Merged

fix error in control methods #107

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2aac698
fix error in control methods
ghar1821 Oct 1, 2025
e71bead
update changelog
ghar1821 Oct 1, 2025
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -97,6 +97,8 @@
* Added EMD vertical global metric and split perfect integration into horizontal and vertical
for computing horizontal and vertical metrics (PR #63).

* Fix problems identified during a full run (PR #99).

## MINOR CHANGES

* Enabled unit tests (PR #2).
Expand Down Expand Up @@ -153,5 +155,6 @@

* Fix missing anndata in yaml file and set the base_r docker image version to 1 instead of 1.0.0 (PR #89).

* Fix bug in control methods (PR #107).


44 changes: 32 additions & 12 deletions src/control_methods/shuffle_integration/script.py
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## VIASH START
par = {
"input_unintegrated": "resources_test/task_cyto_batch_integration/mouse_spleen_flow_cytometry_subset/unintegrated_censored.h5ad",
"output": "output.h5ad",
"input_unintegrated": "resources_test/task_cyto_batch_integration/mouse_spleen_flow_cytometry_subset/unintegrated.h5ad",
"output_integrated_split1": "resources_test/task_cyto_batch_integration/mouse_spleen_flow_cytometry_subset/control_integrated_split1.h5ad",
"output_integrated_split2": "resources_test/task_cyto_batch_integration/mouse_spleen_flow_cytometry_subset/control_integrated_split2.h5ad",
}
meta = {"name": "harmonypy"}
meta = {"name": "shuffle_integration_by_cell_type", "resources_dir": "src/control_methods"}
## VIASH END

print("Importing helper functions", flush=True)
Expand All @@ -16,25 +17,44 @@

print("Reading and preparing input files", flush=True)
adata = ad.read_h5ad(par["input_unintegrated"])
adata_split1 = adata[(adata.obs.is_control > 0) | (adata.obs.split == 1)].copy()
adata_split2 = adata[(adata.obs.is_control > 0) | (adata.obs.split == 2)].copy()

adata.obs["batch_str"] = adata.obs["batch"].astype(str)

print("Randomise features", flush=True)
print("Randomise features - split 1", flush=True)
adata_split1.obs["batch_str"] = adata_split1.obs["batch"].astype(str)
integrated = _randomize_features(
adata.layers["preprocessed"]
adata_split1.layers["preprocessed"]
)

# create new anndata
output = ad.AnnData(
obs=adata.obs[[]],
var=adata.var[[]],
output_split1 = ad.AnnData(
obs=adata_split1.obs[[]],
var=adata_split1.var[[]],
layers={"integrated": integrated},
uns={
"dataset_id": adata_split1.uns["dataset_id"],
"method_id": meta["name"],
"parameters": {},
},
)

print("Randomise features - split 2", flush=True)
adata_split2.obs["batch_str"] = adata_split2.obs["batch"].astype(str)
integrated = _randomize_features(
adata_split2.layers["preprocessed"]
)
# create new anndata
output_split2 = ad.AnnData(
obs=adata_split2.obs[[]],
var=adata_split2.var[[]],
layers={"integrated": integrated},
uns={
"dataset_id": adata.uns["dataset_id"],
"dataset_id": adata_split2.uns["dataset_id"],
"method_id": meta["name"],
"parameters": {},
},
)

print("Write output AnnData to file", flush=True)
output.write_h5ad(par["output"], compression="gzip")
output_split1.write_h5ad(par["output_integrated_split1"], compression="gzip")
output_split2.write_h5ad(par["output_integrated_split2"], compression="gzip")
2 changes: 1 addition & 1 deletion src/control_methods/shuffle_integration_by_batch/script.py
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print("Reading and preparing input files", flush=True)
adata = ad.read_h5ad(par["input_unintegrated"])
adata_split1 = adata[(adata.obs.is_control > 0) | (adata.obs.batch == 1)].copy()
adata_split1 = adata[(adata.obs.is_control > 0) | (adata.obs.split == 1)].copy()
adata_split2 = adata[(adata.obs.is_control > 0) | (adata.obs.split == 2)].copy()

print("Randomise features - split 1", flush=True)
Expand Down
7 changes: 4 additions & 3 deletions src/control_methods/shuffle_integration_by_cell_type/script.py
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Expand Up @@ -5,9 +5,10 @@
## VIASH START
par = {
"input_unintegrated": "resources_test/task_cyto_batch_integration/mouse_spleen_flow_cytometry_subset/unintegrated.h5ad",
"output": "output.h5ad",
"output_integrated_split1": "resources_test/task_cyto_batch_integration/mouse_spleen_flow_cytometry_subset/control_integrated_split1.h5ad",
"output_integrated_split2": "resources_test/task_cyto_batch_integration/mouse_spleen_flow_cytometry_subset/control_integrated_split2.h5ad",
}
meta = {"name": "harmonypy"}
meta = {"name": "shuffle_integration_by_cell_type", "resources_dir": "src/control_methods"}
## VIASH END

print("Importing helper functions", flush=True)
Expand All @@ -16,7 +17,7 @@

print("Reading and preparing input files", flush=True)
adata = ad.read_h5ad(par["input_unintegrated"])
adata_split1 = adata[(adata.obs.is_control > 0) | (adata.obs.batch == 1)].copy()
adata_split1 = adata[(adata.obs.is_control > 0) | (adata.obs.split == 1)].copy()
adata_split2 = adata[(adata.obs.is_control > 0) | (adata.obs.split == 2)].copy()

print("Randomise features - split 1", flush=True)
Expand Down