#27 enabled shap plots

nch-igm · Sep 6, 2021 · 9f4f0d2 · 9f4f0d2
1 parent 38f70f2
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Showing 3 changed files with 12 additions and 47 deletions.
diff --git a/clin_msi/msi_model_scripts/apply_msi_model.py b/clin_msi/msi_model_scripts/apply_msi_model.py
@@ -130,11 +130,11 @@ def apply_model(infile,moddir,outfile,shap_plot_dir=None):
     df=df.rename(columns={sampcol:'samp'})
     dfnew,shapdict,curfeats=apply_mod_to_dataframe(df,moddir)
     dfnew[['samp','yprob']].to_csv(outfile,index=False)
-    # ## GRAB  SHAP DATA
-    # testdat,bmdict=grab_shap_data(dfnew,shapdict,curfeats)
-    # ## EXPORT SHAP PLOTS
-    # for i in range(len(testdat)):
-    #     shap_outfile=shap_plot_dir+"/shap_plot_"+str(i+1)+'.png'
-    #     shaprec=testdat.iloc[i]
-    #     shapdict_loc=bmdict[i]
-    #     build_n_save_shap_plot(shaprec,shapdict_loc,shap_outfile)
+    ## GRAB  SHAP DATA
+    testdat,bmdict=grab_shap_data(dfnew,shapdict,curfeats)
+    ## EXPORT SHAP PLOTS
+    for i in range(len(testdat)):
+        shap_outfile=shap_plot_dir+"/shap_plot_"+str(i+1)+'.png'
+        shaprec=testdat.iloc[i]
+        shapdict_loc=bmdict[i]
+        build_n_save_shap_plot(shaprec,shapdict_loc,shap_outfile)
diff --git a/clin_msi/msi_training.py b/clin_msi/msi_training.py
diff --git a/clin_msi/predict.py b/clin_msi/predict.py
@@ -6,8 +6,8 @@
 import pysam
 import pandas as pd
 
-from .count_normalization.normalize_counts import parse_raw_data
-from .msi_model_scripts.apply_msi_model import apply_model
+from count_normalization.normalize_counts import parse_raw_data
+from msi_model_scripts.apply_msi_model import apply_model
 
 
 def repeat_finder(s):
@@ -96,7 +96,7 @@ def predict(
 
     #apply model to normalized msi counts
     final_results_file = os.path.join(output_dir, sample_name + '_MSIscore.txt')
-    apply_model(os.path.join(output_dir, sample_name + '_normalized.csv'), model_dir, final_results_file)
+    apply_model(os.path.join(output_dir, sample_name + '_normalized.csv'), model_dir, final_results_file,shap_plot_dir=output_dir)
 
 if __name__ == '__main__':
-    predict()
+    predict()