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U53 #33

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merged 2 commits into from
Mar 31, 2023
Merged

U53 #33

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7a89b8f
Add parameter volume for Docker for SBS96, SBS288, ID83, and DBS78.
mdbarnesUCSD Mar 31, 2023
7c1038e
Upgrade to v1.3.12
mdbarnesUCSD Mar 31, 2023
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2 changes: 1 addition & 1 deletion setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ def readme():
with open('README.rst') as f:
return(f.read())

VERSION = '1.3.11'
VERSION = '1.3.12'

def write_version_py(filename='sigProfilerPlotting/version.py'):
# Copied from numpy setup.py
Expand Down
27 changes: 16 additions & 11 deletions sigProfilerPlotting/sigProfilerPlotting.py
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Original file line number Diff line number Diff line change
Expand Up @@ -113,17 +113,20 @@ def get_default_96labels():
result=[outter_bracket[f%16][0]+"["+inner_bracket[f]+"]"+outter_bracket[f%16][1] for f in range(0,96)]
return result

def make_pickle_file(context='SBS96', return_plot_template=False):
def make_pickle_file(context='SBS96', return_plot_template=False, volume=None):

path=os.path.join(SPP_TEMPLATES,context+'.pkl')
if volume is None:
volume = SPP_TEMPLATES

path=os.path.join(volume,context+'.pkl')

# if the pickle file already exists, return the template
if os.path.exists(path):
return pickle.load(open(path, "rb"))

# check if the template directory exists, create if not
if not os.path.exists(SPP_TEMPLATES):
os.mkdir(SPP_TEMPLATES)
if not os.path.exists(volume):
os.mkdir(volume)

if context == 'SBS96':
plot_custom_text = False
Expand Down Expand Up @@ -996,7 +999,8 @@ def plot(counts, labels, sample, project, percentage, aggregate=False, write_to_

def plotSBS(matrix_path, output_path, project, plot_type, percentage=False,
custom_text_upper=None, custom_text_middle=None,
custom_text_bottom=None, savefig_format="pdf"):
custom_text_bottom=None, savefig_format="pdf",
volume=None):
"""Use an input matrix to create a SBS plot.

Args:
Expand All @@ -1005,6 +1009,7 @@ def plotSBS(matrix_path, output_path, project, plot_type, percentage=False,
project: Name of unique sample set
plot_type: Context of the mutational matrix (ie. 96, 288, 384, 1536)
savefig_format: Format of the output plot (pdf, png, or PIL_Image)
volume: Path to the .pkl file containing the plot template. For Docker.
Returns:
Plot of the given input matrix.
"""
Expand All @@ -1019,7 +1024,7 @@ def plotSBS(matrix_path, output_path, project, plot_type, percentage=False,
sample_count = 0

buf= io.BytesIO()
fig_orig=make_pickle_file(context='SBS96', return_plot_template=True)
fig_orig=make_pickle_file(context='SBS96', return_plot_template=True, volume=volume)
pickle.dump(fig_orig, buf)

figs={}
Expand Down Expand Up @@ -3286,7 +3291,7 @@ def plotSBS(matrix_path, output_path, project, plot_type, percentage=False,

data,tsb_mats = reindex_sbs288(data)
buf= io.BytesIO()
fig_orig=make_pickle_file(context='SBS288', return_plot_template=True)
fig_orig=make_pickle_file(context='SBS288', return_plot_template=True, volume=volume)
pickle.dump(fig_orig, buf)

figs = {}
Expand Down Expand Up @@ -3781,7 +3786,7 @@ def plotSBS(matrix_path, output_path, project, plot_type, percentage=False,
print("The provided plot_type:", plot_type, "is not supported by this plotting function")


def plotID(matrix_path, output_path, project, plot_type, percentage=False, custom_text_upper=None, custom_text_middle=None, custom_text_bottom=None, savefig_format = "pdf"):
def plotID(matrix_path, output_path, project, plot_type, percentage=False, custom_text_upper=None, custom_text_middle=None, custom_text_bottom=None, savefig_format = "pdf", volume=None):

plot_custom_text = False
sig_probs = False
Expand All @@ -3793,7 +3798,7 @@ def plotID(matrix_path, output_path, project, plot_type, percentage=False, custo
try:
sample_count = 0
buf= io.BytesIO()
fig_orig=make_pickle_file(context='ID83', return_plot_template=True)
fig_orig=make_pickle_file(context='ID83', return_plot_template=True, volume=volume)
pickle.dump(fig_orig, buf)
figs={}
colors = [[253/256,190/256,111/256], [255/256,128/256,2/256], [176/256,221/256,139/256], [54/256,161/256,46/256],
Expand Down Expand Up @@ -4533,7 +4538,7 @@ def plotID(matrix_path, output_path, project, plot_type, percentage=False, custo
else:
print("The provided plot_type:", plot_type, "is not supported by this plotting function")

def plotDBS(matrix_path, output_path, project, plot_type, percentage=False, custom_text_upper=None, custom_text_middle=None, custom_text_bottom=None,savefig_format='pdf'):
def plotDBS(matrix_path, output_path, project, plot_type, percentage=False, custom_text_upper=None, custom_text_middle=None, custom_text_bottom=None,savefig_format='pdf', volume=None):

plot_custom_text = False
pcawg = False
Expand Down Expand Up @@ -4575,7 +4580,7 @@ def plotDBS(matrix_path, output_path, project, plot_type, percentage=False, cust


buf= io.BytesIO()
fig_orig=make_pickle_file(context='DBS78', return_plot_template=True)
fig_orig=make_pickle_file(context='DBS78', return_plot_template=True, volume=volume)
pickle.dump(fig_orig, buf)

figs={}
Expand Down