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Merge pull request #74 from AlexandrovLab/u45
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U45
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@mdbarnesUCSD
mdbarnesUCSD authored Feb 6, 2023
2 parents 77fd74d + 96be0ea commit 9a72fae
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Showing 2 changed files with 54 additions and 52 deletions.
99 changes: 51 additions & 48 deletions SigProfilerAssignment/DecompositionPlots/PlotDecomposition.py
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Original file line number Diff line number Diff line change
Expand Up @@ -123,24 +123,27 @@ def install_cosmic_plots(context_type="96", genome_build="GRCh37", cosmic_versio
if context_type_str == "SBS":
cosmic_buff_plots = sigPlt.plotSBS(cosmic_file_path, "buffer",
"buffer", cosmic_mtype, percentage=True,
savefig_format="buffer_stream")
savefig_format="PIL_Image")
elif context_type_str == "DBS":
cosmic_mtx = pd.read_csv(cosmic_file_path, sep="\t")
cosmic_buff_plots = sigPlt.plotDBS(cosmic_mtx, "buffer",
"buffer", cosmic_mtype, percentage=True,
savefig_format="buffer_stream")
savefig_format="PIL_Image")
elif context_type_str == "ID":
cosmic_buff_plots = sigPlt.plotID(cosmic_file_path, "buffer",
"buffer", cosmic_mtype, percentage=True,
savefig_format="buffer_stream")
savefig_format="PIL_Image")

# Process the plots to be stored in JSON file
cosmic_img_dict = {}
for tmp_plot in cosmic_buff_plots.keys():
# start at beggining of binary file
# Convert to bytesIO and encode to base64
plot_bytes = io.BytesIO()
seek_start = cosmic_buff_plots[tmp_plot].seek(0)
encoded = base64.b64encode(cosmic_buff_plots[tmp_plot].getvalue())
cosmic_buff_plots[tmp_plot].save(plot_bytes, "png")
encoded = base64.b64encode(plot_bytes.getvalue())
cosmic_img_dict[tmp_plot] = encoded.decode('ascii')
plot_bytes.close()

# JSON output processing
json_object = json.dumps(cosmic_img_dict)
Expand All @@ -152,22 +155,13 @@ def install_cosmic_plots(context_type="96", genome_build="GRCh37", cosmic_versio
exome_str, "have been successfully installed.")
return cosmic_buff_plots


# Helper function for converting BytesIO to image so it can be plotted by reportlab
def bytes_to_img(byte_png):
byte_png.seek(0)
tmp_im=Image.open(byte_png)
image = ImageReader(tmp_im)
return image

# Helper function to convert byte array to image array
def open_byte_to_img_dict(byte_dict):

img_dict = dict()
for name in byte_dict.keys():
tmp_img = bytes_to_img(byte_dict[name])
img_dict[name] = tmp_img
return img_dict
# Convert array of Images to ImageReader array for ReportLab
def convert_to_imgReaderDict(image_dict):
imgReader_dict = dict()
for name in image_dict.keys():
imgReader_dict[name] = ImageReader(image_dict[name])
return imgReader_dict

def calculate_similarities(denovo, denovo_name, est_denovo):
from numpy import inf
Expand Down Expand Up @@ -240,33 +234,33 @@ def genSBS_pngs(denovo_mtx, basis_mtx, output_path, project, mtype, ss_decomp=Fa
percentage=True)
if basis_mtx is not None:
basis_plots = sigPlt.plotSBS(basis_mtx, output_path, project, "96",
percentage=True, savefig_format="buffer_stream")
percentage=True, savefig_format="PIL_Image")
elif mtype == "96":
denovo_plots = sigPlt.plotSBS(denovo_mtx, output_path, project, mtype,
percentage=(not ss_decomp), savefig_format="buffer_stream")
percentage=(not ss_decomp), savefig_format="PIL_Image")
if basis_mtx is not None:
basis_plots = sigPlt.plotSBS(basis_mtx, output_path, project, mtype,
percentage=True, savefig_format="buffer_stream")
percentage=True, savefig_format="PIL_Image")
return denovo_plots,basis_plots

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,
percentage=True, savefig_format="buffer_stream")
percentage=True, savefig_format="PIL_Image")
if basis_mtx is not None:
basis_plots = sigPlt.plotDBS(basis_mtx, output_path, project, mtype,
percentage=True, savefig_format="buffer_stream")
percentage=True, savefig_format="PIL_Image")
return denovo_plots,basis_plots

def genID_pngs(denovo_mtx, basis_mtx, output_path, project, mtype):
denovo_plots = dict()
basis_plots = dict()
denovo_plots = sigPlt.plotID(denovo_mtx, output_path, project, mtype,
percentage=True, savefig_format="buffer_stream")
percentage=True, savefig_format="PIL_Image")
if basis_mtx is not None:
basis_plots = sigPlt.plotID(basis_mtx, output_path, project, mtype,
percentage=True, savefig_format="buffer_stream")
percentage=True, savefig_format="PIL_Image")
return denovo_plots,basis_plots

def genCNV_pngs(denovo_mtx, basis_mtx, output_path, project, mtype):
Expand Down Expand Up @@ -314,33 +308,39 @@ def gen_sub_plots(denovo_mtx, basis_mtx, output_path, project, mtype, ss_decomp)


# generate the plot for the reconstruction
def gen_reconstructed_png_percent(denovo_name, basis_mtx, basis_names, weights, output_path, project, mtype):
def gen_reconstructed_png_percent(denovo_name, basis_mtx, basis_names,
weights, output_path, project, mtype):
reconstruction_plot=dict()
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 = 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", percentage=True, savefig_format='buffer_stream')
reconstruction_plot=sigPlt.plotSBS(reconstruction_mtx,
output_path, "reconstruction_" + project, "96",
percentage=True, savefig_format='PIL_Image')
else:
reconstruction_plot=sigPlt.plotSBS(reconstruction_mtx, output_path, \
"reconstruction_" + project, mtype, percentage=True, savefig_format='buffer_stream')
reconstruction_plot=sigPlt.plotSBS(reconstruction_mtx, output_path,
"reconstruction_" + project, mtype, percentage=True,
savefig_format='PIL_Image')
elif mtype in DBS_CONTEXTS:
reconstruction_plot=sigPlt.plotDBS(reconstruction_mtx, output_path,
"reconstruction_" + project, mtype, percentage=True, savefig_format='buffer_stream')
"reconstruction_" + project, mtype, percentage=True,
savefig_format='PIL_Image')
elif mtype in ID_CONTEXTS:
reconstruction_plot=sigPlt.plotID(reconstruction_mtx, output_path,
"reconstruction_" + project, mtype, percentage=True, savefig_format='buffer_stream')
"reconstruction_" + project, mtype, percentage=True,
savefig_format='PIL_Image')
elif mtype in CNV_CONTEXTS:
reconstruction_plot = sigPlt.plotCNV(reconstruction_mtx, output_path, "reconstruction_"+project, plot_type="pdf", \
percentage=True, aggregate=False, read_from_file=False, write_to_file=False)
reconstruction_plot = sigPlt.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.")

Expand All @@ -366,13 +366,13 @@ def gen_reconstructed_png_numerical(denovo_mtx, denovo_name, basis_mtx, basis_na
else:
reconstruction_plot=sigPlt.plotSBS(reconstruction_mtx, output_path,
"reconstruction_" + project, mtype, percentage=False,
savefig_format="buffer_stream")
savefig_format="PIL_Image")
elif mtype in DBS_CONTEXTS:
reconstruction_plot=sigPlt.plotDBS(reconstruction_mtx, output_path,
"reconstruction_" + project, mtype, percentage=False, savefig_format="buffer_stream")
"reconstruction_" + project, mtype, percentage=False, savefig_format="PIL_Image")
elif mtype in ID_CONTEXTS:
reconstruction_plot=sigPlt.plotID(reconstruction_mtx, output_path,
"reconstruction_" + project, mtype, percentage=False, savefig_format="buffer_stream")
"reconstruction_" + project, mtype, percentage=False, savefig_format="PIL_Image")
elif mtype in CNV_CONTEXTS:
reconstruction_plot = sigPlt.plotCNV(reconstruction_mtx, output_path,
"reconstruction_"+project, plot_type="pdf", percentage=True,
Expand Down Expand Up @@ -510,24 +510,26 @@ def run_PlotDecomposition(denovo_mtx, denovo_name, basis_mtx, basis_names,
present_sigs=np.array(basis_mtx[basis_names])
reconstructed_mtx = np.dot(present_sigs,nonzero_exposures)
# Convert dictionary of bytes to dictionary of images
denovo_plots_dict = open_byte_to_img_dict(denovo_plots_dict)
denovo_plots_dict = convert_to_imgReaderDict(denovo_plots_dict)
# Load in the COSMIC plots
if mtype != "48":
basis_plots_dict = install_cosmic_plots(context_type=mtype,
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)
basis_plots_dict = convert_to_imgReaderDict(basis_plots_dict)
# Generate the reconstruction plot
reconstruction_plot_dict = open_byte_to_img_dict(reconstruction_plot_dict)
reconstruction_plot_dict = convert_to_imgReaderDict(reconstruction_plot_dict)
# Get the reconstruction statistics
statistics=calculate_similarities(denovo_mtx, denovo_name, reconstructed_mtx)
# Return the decomposition plot as a byte array
byte_plot = gen_decomposition(denovo_name, basis_names, weights, output_path, project,
mtype, denovo_plots_dict, basis_plots_dict, reconstruction_plot_dict,
reconstruction=True, statistics=statistics, cosmic_version=cosmic_version,
custom_text=custom_text)

# Clear the plotting memory
sigPlt.clear_plotting_memory()

return byte_plot

# context="96", genome_build="GRCh37", cosmic_version="3.3", exome=False
Expand Down Expand Up @@ -590,18 +592,19 @@ def run_PlotSSDecomposition(denovo_mtx, denovo_name, basis_mtx, basis_names, \
denovo_mtx, denovo_name, basis_mtx,
basis_names, weights, output_path, project, context_type)

denovo_plots_dict = open_byte_to_img_dict(denovo_plots_dict)
denovo_plots_dict = convert_to_imgReaderDict(denovo_plots_dict)
# subset basis_plots_dict to only the plots used
basis_plots_dict = {key: basis_plots_dict[key] for key in basis_names}
basis_plots_dict = open_byte_to_img_dict(basis_plots_dict)
basis_plots_dict = convert_to_imgReaderDict(basis_plots_dict)

reconstruction_plot_dict = open_byte_to_img_dict(reconstruction_plot_dict)
reconstruction_plot_dict = convert_to_imgReaderDict(reconstruction_plot_dict)

statistics=calculate_similarities(denovo_mtx, denovo_name, reconstructed_mtx[denovo_name])
byte_plot = gen_decomposition(denovo_name, basis_names, weights, output_path, project,
context_type, denovo_plots_dict, basis_plots_dict, reconstruction_plot_dict,
reconstruction=True, statistics=statistics, cosmic_version=cosmic_version,
custom_text=custom_text)

# Clear the plotting memory
sigPlt.clear_plotting_memory()

return byte_plot
7 changes: 3 additions & 4 deletions setup.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
if os.path.exists("dist"):
shutil.rmtree("dist")

VERSION = '0.0.25'
VERSION = '0.0.26'


def write_version_py(filename='SigProfilerAssignment/version.py'):
Expand All @@ -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 = 'v0.0.25: DBS Decomposition Plots Plotting'
Update = 'v0.0.26: Clear decomposition plots from memory'
"""
Expand All @@ -31,8 +31,7 @@ def write_version_py(filename='SigProfilerAssignment/version.py'):
'numpy>=1.21.2',
'pandas>=1.2.4',
'SigProfilerMatrixGenerator>=1.2.13',
'sigProfilerPlotting>=1.3.10',
'pillow>=9.1.1',
'sigProfilerPlotting>=1.3.11',
'statsmodels>=0.9.0',
'scikit-learn>=0.24.2',
'psutil>=5.6.1',
Expand Down

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