Merge pull request #60 from AlexandrovLab/decomp_plot_fix

Decomp plot fix

Author: mdbarnesUCSD

SigProfilerAssignment/DecompositionPlots/PlotDecomposition.py

@@ -444,7 +444,9 @@ def gen_decomposition(denovo_name, basis_names, weights, output_path, project, \
 
 
 def run_PlotDecomposition(denovo_mtx, denovo_name, basis_mtx, basis_names,
-		weights, nonzero_exposures, output_path, project, mtype, cosmic_version=None, custom_text=None):
+		weights, nonzero_exposures, output_path, project, mtype,
+		cosmic_version="3.3", genome_build="GRCh37", exome=False,
+		custom_text=None):
 	"""
 	Generates a decomposition plot of the denovo_mtx using the basis_mtx.
 
@@ -499,8 +501,8 @@ def run_PlotDecomposition(denovo_mtx, denovo_name, basis_mtx, basis_names,
 	# Load in the COSMIC plots
 	if mtype != "48":
 		basis_plots_dict = install_cosmic_plots(context_type=mtype,
-				genome_build="GRCh37", cosmic_version="3.3",
-				exome=False)
+				genome_build=genome_build, cosmic_version=cosmic_version,
+				exome=exome)
 		basis_plots_dict = {key: basis_plots_dict[key] for key in basis_names}
 	basis_plots_dict = open_byte_to_img_dict(basis_plots_dict)
 	# Generate the reconstruction plot
@@ -568,7 +570,7 @@ def run_PlotSSDecomposition(denovo_mtx, denovo_name, basis_mtx, basis_names, \
 	# Load in the COSMIC plots
 	basis_plots_dict = install_cosmic_plots(context_type=context_type,
 			genome_build=genome_build, cosmic_version=cosmic_version,
-			exome=False)
+			exome=exome)
 
 	# Create reconstructed matrix and plot
 	reconstructed_mtx,reconstruction_plot_dict = gen_reconstructed_png_numerical(

SigProfilerAssignment/decompose_subroutines.py

@@ -399,7 +399,11 @@ def signature_decomposition(signatures, mtype, directory, genome_build="GRCh37",
             basis_cols = basis_names.copy()
             basis_cols.insert(0,cosmic_mut_types_col)
             denovo_cols=[denovo_mut_types_col, denovo_name]
-            byte_plot = sp.run_PlotDecomposition(originalProcessAvg[denovo_cols], denovo_name, cosmic_sigs_DF[basis_cols], basis_names, weights, nonzero_exposures/5000, directory, "test", mtype_par)
+            byte_plot = sp.run_PlotDecomposition(originalProcessAvg[denovo_cols],
+                        denovo_name, cosmic_sigs_DF[basis_cols], basis_names, weights,
+                        nonzero_exposures/5000, directory, "test", mtype_par,
+                        cosmic_version=cosmic_version, genome_build=genome_build,
+                        exome=exome)
             merger.append(byte_plot)
             with alive_bar(1, ctrl_c=False,bar='blocks', title=f'Decompositon Plot:{denovo_name}') as bar:
                 bar()

SigProfilerAssignment/decomposition.py

@@ -44,7 +44,7 @@ def convert_PDF_to_PNG(input_file_name, output_directory, page_names):
         pix.save(out_file_name)
 
 # Create sample reconstruction plots
-def generate_sample_reconstruction(cosmic_sigs, samples_input, activities, output_dir):
+def generate_sample_reconstruction(cosmic_sigs, samples_input, activities, output_dir, execution_parameters):
     project = "test_run"
     mtype="96"
 
@@ -71,7 +71,10 @@ def generate_sample_reconstruction(cosmic_sigs, samples_input, activities, outpu
                     weights,
                     output_dir,
                     project,
-                    mtype)
+                    mtype,
+                    genome_build = execution_parameters["reference_genome"],
+                    cosmic_version = str(execution_parameters["cosmic_version"]),
+                    exome = execution_parameters["exome"])
         final_pdf.append(result)
 
     pdf_output_path = os.path.join(output_dir,
@@ -659,7 +662,8 @@ def spa_analyze(samples, output, input_type='matrix', context_type="96", signatu
         generate_sample_reconstruction(cosmic_sig_ref,
                                         genomes,
                                         cosmic_activities,
-                                        ss_recon_odir)
+                                        ss_recon_odir,
+                                        execution_parameters)
 
     # Complete JOB_METADATA
     sysdata = open(output+"/JOB_METADATA.txt", "a")

setup.py

@@ -6,7 +6,7 @@
 if os.path.exists("dist"):
     shutil.rmtree("dist")
 
-VERSION = '0.0.20'
+VERSION = '0.0.21'
 
 
 def write_version_py(filename='SigProfilerAssignment/version.py'):
@@ -15,7 +15,7 @@ def write_version_py(filename='SigProfilerAssignment/version.py'):
 # THIS FILE IS GENERATED FROM SigProfilerAssignment SETUP.PY
 short_version = '%(version)s'
 version = '%(version)s'
-Update = 'Implement sample reconstruction plot'
+Update = 'Resolve reference signature default value issue for decomposition plots.'
 
     
     """