def genDBS_pngs(denovo_mtx, basis_mtx, output_path, project, mtype):
denovo_plots = dict()
basis_plots = dict()
denovo_plots = sigPlt.plotDBS(denovo_mtx, output_path, project, mtype,
True)
basis_plots = sigPlt.plotDBS(basis_mtx, output_path, project, mtype, True)
return denovo_plots, basis_plots
def genSBS_pngs(denovo_mtx, basis_mtx, output_path, project, mtype):
denovo_plots = dict()
basis_plots = dict()
if mtype == "1536" or mtype == "288":
denovo_plots = sigPlt.plotSBS(denovo_mtx, output_path, project, mtype,
True)
basis_plots = sigPlt.plotSBS(basis_mtx, output_path, project, "96",
True)
elif mtype == "96":
denovo_plots = sigPlt.plotSBS(denovo_mtx, output_path, project, mtype,
True)
basis_plots = sigPlt.plotSBS(basis_mtx, output_path, project, mtype,
True)
return denovo_plots, basis_plots
def gen_reconstructed_png(denovo_name, basis_mtx, basis_names, weights,
output_path, project, mtype):
col_names = [denovo_name]
mut_col = basis_mtx.iloc[:, 0]
recon_plot = basis_mtx[basis_names[0]] * float(weights[0].strip("%")) / 100
for i in range(1, len(weights)):
recon_plot = recon_plot + basis_mtx[basis_names[i]] * (
float(weights[i].strip("%")) / 100)
recon_plot = pd.Series(recon_plot, name=denovo_name)
reconstruction_mtx = pd.concat([mut_col, recon_plot], axis=1)
if mtype in SBS_CONTEXTS:
if mtype == "1536":
sigPlt.plotSBS(reconstruction_mtx, output_path,
"reconstruction_" + project, "96", True)
else:
sigPlt.plotSBS(reconstruction_mtx, output_path,
"reconstruction_" + project, mtype, True)
elif mtype in DBS_CONTEXTS:
sigPlt.plotDBS(reconstruction_mtx, output_path,
"reconstruction_" + project, mtype, True)
elif mtype in ID_CONTEXTS:
sigPlt.plotID(reconstruction_mtx, output_path,
"reconstruction_" + project, mtype, True)
else:
print(type(mtype))
print("ERROR: mtype is " + mtype + " and is not yet supported.")
return reconstruction_mtx
def genSBS_pngs(denovo_mtx, basis_mtx, output_path, project, mtype):
if mtype == "1536":
sigPlt.plotSBS(denovo_mtx, output_path, project, mtype, True)
sigPlt.plotSBS(basis_mtx, output_path, project, "96", True)
else:
sigPlt.plotSBS(denovo_mtx, output_path, project, mtype, True)
sigPlt.plotSBS(basis_mtx, output_path, project, mtype, True)
def gen_reconstructed_png(denovo_name, basis_mtx, basis_names, weights,
output_path, project, mtype):
reconstruction_plot = dict()
col_names = [denovo_name]
mut_col = basis_mtx.iloc[:, 0]
recon_plot = basis_mtx[basis_names[0]] * float(weights[0].strip("%")) / 100
for i in range(1, len(weights)):
recon_plot = recon_plot + basis_mtx[basis_names[i]] * (
float(weights[i].strip("%")) / 100)
recon_plot = pd.Series(recon_plot, name=denovo_name)
reconstruction_mtx = pd.concat([mut_col, recon_plot], axis=1)
if mtype in SBS_CONTEXTS:
if mtype == "1536" or mtype == "288":
reconstruction_plot = sigPlt.plotSBS(reconstruction_mtx,
output_path,
"reconstruction_" + project,
"96", True)
else:
reconstruction_plot = sigPlt.plotSBS(reconstruction_mtx,
output_path,
"reconstruction_" + project,
mtype, True)
elif mtype in DBS_CONTEXTS:
reconstruction_plot = sigPlt.plotDBS(reconstruction_mtx, output_path,
"reconstruction_" + project,
mtype, True)
elif mtype in ID_CONTEXTS:
reconstruction_plot = sigPlt.plotID(reconstruction_mtx, output_path,
"reconstruction_" + project, mtype,
True)
elif mtype in CNV_CONTEXTS:
reconstruction_plot = pltCNV.plotCNV(reconstruction_mtx, output_path, "reconstruction_"+project, plot_type="pdf", \
percentage=True, aggregate=False, read_from_file=False, write_to_file=False)
else:
print("ERROR: mtype is " + mtype + " and is not yet supported.")
return reconstruction_mtx, reconstruction_plot
def genID_pngs(denovo_mtx, basis_mtx, output_path, project, mtype):
sigPlt.plotID(denovo_mtx, output_path, project, mtype, True)
sigPlt.plotID(basis_mtx, output_path, project, mtype, True)
def genDBS_pngs(denovo_mtx, basis_mtx, output_path, project, mtype):
sigPlt.plotDBS(denovo_mtx, output_path, project, mtype, True)
sigPlt.plotDBS(basis_mtx, output_path, project, mtype, True)