Merge pull request #118 from Teichlab/develop

Develop
Teichlab · Sep 9, 2019 · 3d62800 · 3d62800
2 parents 91b9c44 + 33a59eb
commit 3d62800
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Showing 3 changed files with 19 additions and 3 deletions.
diff --git a/cellphonedb/src/core/methods/method_launcher.py b/cellphonedb/src/core/methods/method_launcher.py
@@ -122,6 +122,7 @@ def _counts_validations(counts: pd.DataFrame, meta: pd.DataFrame) -> pd.DataFram
             counts = counts.astype(pd.np.float)  # type: pd.DataFrame
         except:
             raise ParseCountsException
+        meta.index = meta.index.astype(str)
         for cell in meta.index.values:
             if cell not in counts.columns.values:
                 raise ParseCountsException('Some cells in meta didnt exist in counts columns',

diff --git a/cellphonedb/src/core/preprocessors/method_preprocessors.py b/cellphonedb/src/core/preprocessors/method_preprocessors.py
@@ -28,6 +28,7 @@ def meta_preprocessor(meta_raw: pd.DataFrame) -> pd.DataFrame:
         meta = pd.DataFrame(data={'cell_type': meta_raw.iloc[:, 1]})
         meta.set_index(meta_raw.iloc[:, 0], inplace=True)
         meta.index.name = 'cell'
+        meta.index = meta.index.astype(str)
         return meta
 
     except:

diff --git a/run_cellphonedb_rabbitmq.py b/run_cellphonedb_rabbitmq.py
@@ -170,30 +170,44 @@ def heatmaps_plot_results(meta: str, pvalues: str, pvalue: float, job_id: str):
                 count_name = 'plot_count__{}.png'.format(job_id)
                 count_log_name = 'plot_count_log__{}.png'.format(job_id)
 
+                count_network_name = 'count_network__{}.txt'.format(job_id)
+                interactions_count_name = 'interactions_count__{}.txt'.format(job_id)
+
                 heatmaps_plot(meta_file=meta_file.name,
                               pvalues_file=pvalues_file.name,
                               output_path=output_path,
                               count_name=count_name,
                               log_name=count_log_name,
+                              count_network_filename=count_network_name,
+                              interaction_count_filename=interactions_count_name,
                               pvalue=pvalue)
 
                 output_count_file = os.path.join(output_path, count_name)
                 output_count_log_file = os.path.join(output_path, count_log_name)
+                output_count_network_file = os.path.join(output_path, count_network_name)
+                output_interactions_count_file = os.path.join(output_path, interactions_count_name)
 
-                if not os.path.exists(output_count_file) or not os.path.exists(output_count_log_file):
-                    raise PlotException('Could not generate output file for plot of type dot_plot')
+                if not os.path.exists(output_count_file) \
+                        or not os.path.exists(output_count_log_file) \
+                        or not os.path.exists(output_count_network_file) \
+                        or not os.path.exists(output_interactions_count_file):
+                    raise PlotException('Could not generate output file for plot of type heatmap_plot')
 
                 response = {
                     'job_id': job_id,
                     'files': {
                         'count_plot': count_name,
-                        'count_log_plot': count_log_name
+                        'count_log_plot': count_log_name,
+                        'count_network': count_network_name,
+                        'interactions_sum': interactions_count_name,
                     },
                     'success': True
                 }
 
                 write_image_to_s3(output_count_file, count_name)
                 write_image_to_s3(output_count_log_file, count_log_name)
+                write_image_to_s3(output_count_network_file, count_network_name)
+                write_image_to_s3(output_interactions_count_file, interactions_count_name)
 
                 return response