Merge pull request #47 from AlexandrovLab/u29

Fix TMB plot y-axis when using exome parameter

Author: marcos-diazg

SigProfilerAssignment/Analyzer.py

@@ -4,8 +4,8 @@ def decompose_fit(samples, output, signatures=None, signature_database=None,nnls
 
                 decomp.spa_analyze(samples=samples,  output=output, signatures=signatures, signature_database=signature_database,nnls_add_penalty=nnls_add_penalty, nnls_remove_penalty=nnls_remove_penalty, initial_remove_penalty=initial_remove_penalty,genome_build=genome_build, cosmic_version=cosmic_version, make_plots=make_plots, collapse_to_SBS96=collapse_to_SBS96,connected_sigs=connected_sigs, verbose=verbose,decompose_fit_option= True,denovo_refit_option=False,cosmic_fit_option=False,devopts=devopts,new_signature_thresh_hold=new_signature_thresh_hold,exclude_signature_subgroups=exclude_signature_subgroups,exome=exome,input_type=input_type,context_type=context_type,export_probabilities=export_probabilities)
 
-def denovo_fit(samples,  output, signatures=None, signature_database=None,nnls_add_penalty=0.05,nnls_remove_penalty=0.01, initial_remove_penalty=0.05, genome_build="GRCh37", cosmic_version=3.3, make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,new_signature_thresh_hold=0.8,input_type='matrix',context_type="96",export_probabilities=True):
-                decomp.spa_analyze(samples=samples,  output=output, signatures=signatures, signature_database=signature_database,nnls_add_penalty=nnls_add_penalty, nnls_remove_penalty=nnls_remove_penalty, initial_remove_penalty=initial_remove_penalty,genome_build=genome_build, cosmic_version=cosmic_version, new_signature_thresh_hold=new_signature_thresh_hold, make_plots=make_plots, collapse_to_SBS96=collapse_to_SBS96,connected_sigs=connected_sigs, verbose=verbose,decompose_fit_option= False,denovo_refit_option=True,cosmic_fit_option=False,devopts=devopts,input_type=input_type,context_type=context_type,export_probabilities=export_probabilities)
+def denovo_fit(samples,  output, signatures=None, signature_database=None,nnls_add_penalty=0.05,nnls_remove_penalty=0.01, initial_remove_penalty=0.05, genome_build="GRCh37", cosmic_version=3.3, make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,new_signature_thresh_hold=0.8,exome=False,input_type='matrix',context_type="96",export_probabilities=True):
+                decomp.spa_analyze(samples=samples,  output=output, signatures=signatures, signature_database=signature_database,nnls_add_penalty=nnls_add_penalty, nnls_remove_penalty=nnls_remove_penalty, initial_remove_penalty=initial_remove_penalty,genome_build=genome_build, cosmic_version=cosmic_version, new_signature_thresh_hold=new_signature_thresh_hold, make_plots=make_plots, collapse_to_SBS96=collapse_to_SBS96,connected_sigs=connected_sigs, verbose=verbose,decompose_fit_option= False,denovo_refit_option=True,cosmic_fit_option=False,devopts=devopts,exome=exome,input_type=input_type,context_type=context_type,export_probabilities=export_probabilities)
 
 def cosmic_fit(samples, output, signatures=None, signature_database=None,nnls_add_penalty=0.05, nnls_remove_penalty=0.01, initial_remove_penalty=0.05,genome_build="GRCh37", cosmic_version=3.3, make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,exclude_signature_subgroups=None,exome=False,input_type='matrix',context_type="96",export_probabilities=True):
                 decomp.spa_analyze(samples=samples,  output=output, signatures=signatures, signature_database=signature_database,nnls_add_penalty=nnls_add_penalty, nnls_remove_penalty=nnls_remove_penalty, initial_remove_penalty=initial_remove_penalty,genome_build=genome_build, cosmic_version=cosmic_version, make_plots=make_plots, collapse_to_SBS96=collapse_to_SBS96,connected_sigs=connected_sigs, verbose=verbose,decompose_fit_option= False,denovo_refit_option=False,cosmic_fit_option=True,devopts=devopts,exclude_signature_subgroups=exclude_signature_subgroups,exome=exome,input_type=input_type,context_type=context_type,export_probabilities=export_probabilities)

SigProfilerAssignment/decomposition.py

@@ -167,7 +167,12 @@ def spa_analyze(samples, output, input_type='matrix', context_type="96", signatu
             os.makedirs(output)
     except:
         print ("The {} folder could not be created".format("output"))
-  
+
+    # Add sequence parameter to control the tmbplot y-axis scale
+    if exome == True:
+        sequence = 'exome'
+    else:
+        sequence = 'genome'
 
                                                                 #################
                                                                 # Denovo refiting #
@@ -251,7 +256,7 @@ def spa_analyze(samples, output, input_type='matrix', context_type="96", signatu
 
         if devopts == None:
             exposureAvg = sub.make_final_solution(processAvg, genomes, allsigids, layer_directory1, mutation_type, index, colnames, 
-                                    cosmic_sigs=True, attribution = attribution, denovo_exposureAvg  = exposureAvg_dummy , 
+                                    cosmic_sigs=True, attribution = attribution, denovo_exposureAvg  = exposureAvg_dummy, sequence=sequence, 
                                     background_sigs=background_sigs, verbose=verbose, genome_build=genome_build, 
                                     add_penalty=nnls_add_penalty, remove_penalty=nnls_remove_penalty,
                                     initial_remove_penalty=init_rem_denovo,connected_sigs=connected_sigs,refit_denovo_signatures=False,
@@ -263,10 +268,9 @@ def spa_analyze(samples, output, input_type='matrix', context_type="96", signatu
             signature_stats = devopts['signature_stats']
             sequence=devopts['sequence']
             processSTE=devopts['processSTE']
-            sequence =devopts['sequence']
 
             exposureAvg = sub.make_final_solution(processAvg, genomes, allsigids, layer_directory1, mutation_type, index, colnames, 
-                                    cosmic_sigs=True, attribution = attribution, denovo_exposureAvg  = exposureAvg_dummy , sequence=sequence, 
+                                    cosmic_sigs=True, attribution = attribution, denovo_exposureAvg  = exposureAvg_dummy, sequence=sequence, 
                                     background_sigs=background_sigs, verbose=verbose, genome_build=genome_build, signature_total_mutations = signature_total_mutations,
                                     add_penalty=nnls_add_penalty, remove_penalty=nnls_remove_penalty, process_std_error = processSTE, signature_stabilities = signature_stabilities,
                                     initial_remove_penalty=init_rem_denovo,connected_sigs=connected_sigs,refit_denovo_signatures=True,export_probabilities=export_probabilities)
@@ -360,7 +364,7 @@ def spa_analyze(samples, output, input_type='matrix', context_type="96", signatu
 
         print("\n Assigning decomposed signature")
         result = sub.make_final_solution(processAvg, genomes, allsigids, layer_directory2, mutation_type, index, colnames, 
-                                cosmic_sigs=True, attribution = attribution, denovo_exposureAvg  = exposureAvg ,  
+                                cosmic_sigs=True, attribution = attribution, denovo_exposureAvg  = exposureAvg, sequence=sequence,  
                                 background_sigs=background_sigs, verbose=verbose, genome_build=genome_build, 
                                 add_penalty=nnls_add_penalty, remove_penalty=nnls_remove_penalty, 
                                 initial_remove_penalty=initial_remove_penalty,connected_sigs=connected_sigs,
@@ -473,7 +477,7 @@ def spa_analyze(samples, output, input_type='matrix', context_type="96", signatu
 
 
         sub.make_final_solution(processAvg, genomes, allsigids, layer_directory3, mutation_type, index, colnames, 
-                            cosmic_sigs=True, attribution = attribution, denovo_exposureAvg  = exposureAvg_dummy ,  
+                            cosmic_sigs=True, attribution = attribution, denovo_exposureAvg  = exposureAvg_dummy, sequence=sequence, 
                             background_sigs=background_sigs, verbose=verbose, genome_build=genome_build, 
                             add_penalty=nnls_add_penalty, remove_penalty=nnls_remove_penalty, 
                             initial_remove_penalty=initial_remove_penalty,connected_sigs=connected_sigs,

setup.py

@@ -6,7 +6,7 @@
 if os.path.exists("dist"):
     shutil.rmtree("dist")
 
-VERSION = '0.0.15'
+VERSION = '0.0.16'
 
 with open('README.md') as f:
 	long_description = f.read()
@@ -17,7 +17,7 @@ def write_version_py(filename='SigProfilerAssignment/version.py'):
 # THIS FILE IS GENERATED FROM SigProfilerAssignment SETUP.PY
 short_version = '%(version)s'
 version = '%(version)s'
-Update = '1. Add subgroups for DBS and ID COSMIC signatures. 2. Add export_probabilities parameter .'
+Update = 'Fix TMB plot y-axis when using exome parameter'
     
     """
     fh = open(filename, 'w')
@@ -29,7 +29,7 @@ def write_version_py(filename='SigProfilerAssignment/version.py'):
           'pandas>=1.2.4', 
           'SigProfilerExtractor>=1.1.14',
           'SigProfilerMatrixGenerator>=1.2.12', 
-          'sigProfilerPlotting>=1.2.2', 
+          'sigProfilerPlotting==1.2.2', 
           'pillow',
           'statsmodels>=0.9.0',
           'scikit-learn>=0.24.2',