celloracle ns fixed

src/exp_analysis/helper.py

@@ -101,35 +101,7 @@ def plot_centrality(self, df, title='',ax=None, xlabel='Degree', ylabel='Gene',
         if colors is not None:
             for label, color in zip(ax.get_yticklabels(), colors):
                 label.set_color(color)
-    def role_analysis(self, top_q=None) -> pd.DataFrame:
-        '''
-            Vester's sensitivity analysis. 
-                - active_sum: active sum. Sum along rows of the influence matrix and it indicates how much does a variable influence all the others.
-                - passive_sum: passive sum. Its is the sum along columns of the influence matrix and it indicates how sensitive a variable is, how does it react to the influence of others
-                - Active: +AS, -PS
-                - Passive: -AS, -PS
-                - Critical: +AS, +PS
-                - neutral: -AS, -PS
-        ------------------------------------------------------
-        inputs: net (DataFrame)
-        top_q: top quantile
-        output: VSA (DataFrame) -> genename: active_sum, passive_sum, Role
-        '''
-        # active sum and passive sum
-        net = self.net.copy()  
-        net = net[net.weight>net.weight.quantile(top_q)]
-        gene_names = np.union1d(net.source.unique(), net.target.unique())
-        active_sum = np.asarray([sum(net.query(f"source == '{gene}'")['weight']) for gene in gene_names])
-        passive_sum = np.asarray([sum(net.query(f"target == '{gene}'")['weight']) for gene in gene_names])
-
-        # define the roles ['Buffering', 'Passive', 'Active', 'Critical'] -> [0, 1, 2, 3]
-        active_sum_threhsold = np.quantile(active_sum, 0.9)
-        passive_sum_threhsold = np.quantile(passive_sum, 0.9)
-        # active_sum, passive_sum = standardize_array(active_sum), standardize_array(passive_sum)
-        roles = [2*as_flag+ps_flag for as_flag, ps_flag in zip(active_sum>active_sum_threhsold, passive_sum>passive_sum_threhsold)]
-        self.roles = pd.DataFrame(data={'gene_name': gene_names, 'active_sum': active_sum, 'passive_sum': passive_sum, 'role':roles })
-        self.roles.set_index('gene_name',inplace=True)
-        return self.roles
+
 
     def top_edges(self, quantile=0.95):
         grn = self.net 

src/methods/multi_omics/celloracle_ns/main.nf

@@ -8,6 +8,7 @@ workflow run_wf {
     | celloracle.run(
       fromState: [multiomics_rna: "multiomics_rna",
               multiomics_atac: "multiomics_atac",
+              tf_all: "tf_all",
               temp_dir: "temp_dir",
               num_workers: "num_workers",
               max_n_links: "max_n_links"

src/methods/multi_omics/celloracle_ns/run.sh

@@ -17,45 +17,26 @@ param_list:
   - id: ${RUN_ID}
     multiomics_rna: ${resources_dir}/grn-benchmark/multiomics_rna.h5ad
     multiomics_atac: ${resources_dir}/grn-benchmark/multiomics_atac.h5ad
+    tf_all: ${resources_dir}/prior/tf_all.csv
     num_workers: $num_workers
     temp_dir: ./tmp/grn
 output_state: "state.yaml"
 publish_dir: "$publish_dir"
 HERE
 
-if [ "$submit" = true ]; then
-  nextflow run . \
-    -main-script  target/nextflow/workflows/grn_inference_celloracle/main.nf \
-    -profile docker \
-    -with-trace \
-    -c src/common/nextflow_helpers/labels_ci.config \
-    -params-file params/${RUN_ID}.yaml
-
-
-  ./tw-windows-x86_64.exe launch `
-        https://github.com/openproblems-bio/task_grn_inference.git `
-        --revision build/main `
-        --pull-latest `
-        --main-script target/nextflow/workflows/run_grn_inference/main.nf `
-        --workspace 53907369739130 `
-        --compute-env 6TeIFgV5OY4pJCk8I0bfOh `
-        --params-file ./params/celloracle_test.yaml `
-        --config src/common/nextflow_helpers/labels_tw.config
-fi 
-
-
-
-if [ "$read_results" = true ]; then 
-    aws s3 sync s3://openproblems-data/resources/grn/results/${RUN_ID} ./resources/results/${RUN_ID} 
-fi
-
-
-./tw-windows-x86_64.exe launch `
-       https://github.com/openproblems-bio/task_grn_inference.git `
-       --revision build/main `
-       --pull-latest `
-       --main-script target/nextflow/workflows/grn_inference_celloracle/main.nf `
-       --workspace 53907369739130 `
-       --compute-env 6TeIFgV5OY4pJCk8I0bfOh `
-       --params-file ./params/celloracle.yaml `
-       --config src/common/nextflow_helpers/labels_tw.config
+# nextflow run . \
+#   -main-script  target/nextflow/workflows/grn_inference_celloracle/main.nf \
+#   -profile docker \
+#   -with-trace \
+#   -c src/common/nextflow_helpers/labels_ci.config \
+#   -params-file params/${RUN_ID}.yaml
+
+
+./tw launch https://github.com/openproblems-bio/task_grn_inference \
+  --revision build/main \
+  --pull-latest \
+  --main-script target/nextflow/workflows/grn_inference_celloracle/main.nf \
+  --workspace 53907369739130 \
+  --compute-env 6TeIFgV5OY4pJCk8I0bfOh \
+  --params-file ${param_file} \
+  --config src/common/nextflow_helpers/labels_tw.config