onedaytime try

scripts/run_baselines.sh

@@ -1,53 +1,63 @@
-echo  "negative control"
-viash run src/control_methods/negative_control/config.vsh.yaml -- --multiomics_rna resources/grn-benchmark/multiomics_rna.h5ad \
-  --perturbation_data resources/grn-benchmark/perturbation_data.h5ad \
-  --tf_all resources/prior/tf_all.csv \
-  --prediction resources/grn_models/baselines/negative_control.csv 
+# echo  "negative control"
+# viash run src/control_methods/negative_control/config.vsh.yaml -- --multiomics_rna resources/grn-benchmark/multiomics_rna.h5ad \
+#   --perturbation_data resources/grn-benchmark/perturbation_data.h5ad \
+#   --tf_all resources/prior/tf_all.csv \
+#   --prediction resources/grn_models/baselines/negative_control.csv 
 
 
-echo  "baseline pearson"
-viash run src/control_methods/baseline_corr/config.vsh.yaml -- --multiomics_rna resources/grn-benchmark/multiomics_rna.h5ad \
-  --tf_all resources/prior/tf_all.csv \
-  --causal false \
-  --corr_method pearson \
-  --cell_type_specific  false \
-  --metacell  false \
-  --impute false \
-  --prediction resources/grn_models/baselines/baseline_pearson.csv 
+# echo  "baseline pearson"
+# viash run src/control_methods/baseline_corr/config.vsh.yaml -- --multiomics_rna resources/grn-benchmark/multiomics_rna.h5ad \
+#   --tf_all resources/prior/tf_all.csv \
+#   --causal false \
+#   --corr_method pearson \
+#   --cell_type_specific  false \
+#   --metacell  false \
+#   --impute false \
+#   --prediction resources/grn_models/baselines/baseline_pearson.csv 
 
-echo  "baseline pearson causal"
-viash run src/control_methods/baseline_corr/config.vsh.yaml -- --multiomics_rna resources/grn-benchmark/multiomics_rna.h5ad \
-  --tf_all resources/prior/tf_all.csv \
-  --causal true \
-  --corr_method pearson \
-  --cell_type_specific  false \
-  --metacell  false \
-  --impute false \
-  --prediction resources/grn_models/baselines/baseline_pearson_causal.csv 
+# echo  "baseline pearson causal"
+# viash run src/control_methods/baseline_corr/config.vsh.yaml -- --multiomics_rna resources/grn-benchmark/multiomics_rna.h5ad \
+#   --tf_all resources/prior/tf_all.csv \
+#   --causal true \
+#   --corr_method pearson \
+#   --cell_type_specific  false \
+#   --metacell  false \
+#   --impute false \
+#   --prediction resources/grn_models/baselines/baseline_pearson_causal.csv 
 
 
-echo  "baseline causal cell type"
-viash run src/control_methods/baseline_corr/config.vsh.yaml -- --multiomics_rna resources/grn-benchmark/multiomics_rna.h5ad \
-  --tf_all resources/prior/tf_all.csv \
-  --causal true \
-  --corr_method pearson \
-  --cell_type_specific  true \
-  --metacell  false \
-  --impute false \
-  --prediction resources/grn_models/baselines/baseline_pearson_causal_celltype.csv 
+# echo  "baseline causal cell type"
+# viash run src/control_methods/baseline_corr/config.vsh.yaml -- --multiomics_rna resources/grn-benchmark/multiomics_rna.h5ad \
+#   --tf_all resources/prior/tf_all.csv \
+#   --causal true \
+#   --corr_method pearson \
+#   --cell_type_specific  true \
+#   --metacell  false \
+#   --impute false \
+#   --prediction resources/grn_models/baselines/baseline_pearson_causal_celltype.csv 
+
+# echo  "baseline pearson causal metacell"
+# viash run src/control_methods/baseline_corr/config.vsh.yaml -- --multiomics_rna resources/grn-benchmark/multiomics_rna.h5ad \
+#   --tf_all resources/prior/tf_all.csv \
+#   --causal true \
+#   --corr_method pearson \
+#   --cell_type_specific  false \
+#   --metacell  true \
+#   --impute false \
+#   --prediction resources/grn_models/baselines/baseline_pearson_causal_metacell.csv 
 
-echo  "baseline pearson causal metacell"
+echo  "baseline pearson causal imputation"
 viash run src/control_methods/baseline_corr/config.vsh.yaml -- --multiomics_rna resources/grn-benchmark/multiomics_rna.h5ad \
   --tf_all resources/prior/tf_all.csv \
   --causal true \
   --corr_method pearson \
   --cell_type_specific  false \
-  --metacell  true \
-  --impute false \
-  --prediction resources/grn_models/baselines/baseline_pearson_causal_metacell.csv 
+  --metacell  false \
+  --impute true \
+  --prediction resources/grn_models/baselines/baseline_pearson_causal_impute.csv 
 
-echo  "positive control"
-viash run src/control_methods/positive_control/config.vsh.yaml -- --multiomics_rna resources/grn-benchmark/multiomics_rna.h5ad \
-  --perturbation_data resources/grn-benchmark/perturbation_data.h5ad \
-  --tf_all resources/prior/tf_all.csv \
-  --prediction resources/grn_models/baselines/positive_control.csv 
+# echo  "positive control"
+# viash run src/control_methods/positive_control/config.vsh.yaml -- --multiomics_rna resources/grn-benchmark/multiomics_rna.h5ad \
+#   --perturbation_data resources/grn-benchmark/perturbation_data.h5ad \
+#   --tf_all resources/prior/tf_all.csv \
+#   --prediction resources/grn_models/baselines/positive_control.csv 

scripts/run_benchmark_single_omics.sh

@@ -3,7 +3,7 @@
 # RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
 RUN_ID="single_omics_inference"
 # resources_dir="./resources_test/"
-resources_dir="s3://openproblems-data/resources/grn"
+resources_dir="s3://openproblems-data/resources_test/grn"
 publish_dir="${resources_dir}/results/${RUN_ID}"
 
 

src/control_methods/baseline_corr/script.py

@@ -93,34 +93,16 @@ def create_meta_cells(df, n_cells=15):
 
 if par['impute']:
     print("imputing")
-    # import magic
-    # import scprep
+    import magic
+    import scprep
 
-    # magic_operator = magic.MAGIC()
+    magic_operator = magic.MAGIC()
 
-    # multiomics_rna = magic_operator.fit_transform(multiomics_rna)
-    from sklearn.impute import KNNImputer
-    import numpy as np
-
-    print("Imputing with KNN")
-
-    # Convert to dense if the matrix is sparse
-    if sc.sparse.issparse(multiomics_rna.X):
-        multiomics_rna_dense = multiomics_rna.X.toarray()
-    else:
-        multiomics_rna_dense = multiomics_rna.X
-
-    # Apply KNN imputation
-    knn_imputer = KNNImputer(n_neighbors=5)  # You can adjust the number of neighbors
-    multiomics_rna_imputed = knn_imputer.fit_transform(multiomics_rna_dense)
-
-    # Update the AnnData object with the imputed values
-    multiomics_rna.X = multiomics_rna_imputed
-    print('zero ration: ', (multiomics_rna.X==0).sum()/multiomics_rna.size)
+    multiomics_rna = magic_operator.fit_transform(multiomics_rna)
+
+    print('zero ration: ', (multiomics_rna.X==0).sum()/multiomics_rna.X.size)
 print('Create corr net')
 net = create_corr_net(multiomics_rna.X, groups, par['corr_method'])
 
-
-
 print('Output GRN')
 net.to_csv(par['prediction'])

src/exp_analysis/test.sh

@@ -1,4 +1,4 @@
 viash run src/exp_analysis/config.vsh.yaml -- \
     --perturbation_data resources/grn-benchmark/perturbation_data.h5ad \
-    --prediction resources/grn_models/genie3.csv \
+    --prediction resources/grn_models/baselines/positive_control.csv \
 

src/methods/single_omics/ennet/config.vsh.yaml

@@ -34,4 +34,4 @@ platforms:
   - type: native
   - type: nextflow
     directives:
-      label: [onedaytime,midmem,midcpu]
+      label: [onedaytime, highmem, midcpu]

src/methods/single_omics/pidc/config.vsh.yaml

@@ -22,4 +22,4 @@ platforms:
   - type: native
   - type: nextflow
     directives:
-      label: [onedaytime, midmem,midcpu]
+      label: [onedaytime, highmem,midcpu]

src/methods/single_omics/scsgl/config.vsh.yaml

@@ -18,8 +18,8 @@ platforms:
     image: apassemi/scsgl
     setup:
       - type: python
-        packages: [ anndata, numba==0.53.1, scipy==1.6.3, pandas==1.2.4, rpy2==3.4.4, numpy==1.20.2, scikit-learn==0.24.1, PyYAML==6.0.2 ]
+        packages: [ anndata, numba==0.53.1, scipy==1.6.3, pandas==1.2.4, rpy2==3.4.4, numpy==1.20.2, scikit-learn==0.24.1, PyYAML==6.0.2, pysrc3==0.1.3 ]
   - type: native
   - type: nextflow
     directives:
-      label: [onedaytime, midmem,midcpu]
+      label: [onedaytime, highmem,midcpu]

src/methods/single_omics/tigress/config.vsh.yaml

@@ -30,4 +30,4 @@ platforms:
   - type: native
   - type: nextflow
     directives:
-      label: [onedaytime, midmem, highcpu]
+      label: [onedaytime, highmem, highcpu]

src/metrics/regression_1/test.sh

@@ -1,5 +1,5 @@
 viash run src/metrics/regression_1/config.vsh.yaml -- \
     --perturbation_data resources/grn-benchmark/perturbation_data.h5ad \
     --tf_all resources/prior/tf_all.csv \
-    --prediction output/baseline_corr.csv \
+    --prediction resources/grn_models/baselines/baseline_pearson_causal_impute.csv \
     --score output/score.h5ad

src/workflows/run_benchmark_single_omics/config.vsh.yaml

@@ -101,4 +101,4 @@ functionality:
 platforms:
   - type: nextflow
     directives:
-      label: [ threedaystime, midmem, highcpu, gpu]
+      label: [ onedaytime, highmem, highcpu, gpu]