def test_data_model_make_01(example_data):
model = DataModel(example_data)
assert model is not None
model.make()
sectors_legend = model.make_sectors_legend()
print(sectors_legend)
def test_data_model_make_01(example_data):
model = DataModel(example_data)
assert model is not None
model.make()
sector_model = SectorsDataModel(model)
sector_model.make()
print(sector_model.column_labels)
print(sector_model.sector)
print(np.argwhere(43 == model.Z['leaves']))
print(np.argmin(model.sector))
m = np.argmin(model.sector)
print(m)
print(model.sector[m])
print(model.column_labels[m])
print(m - 1)
print(model.sector[m - 1])
print(model.column_labels[m - 1])
assert sector_model.sector[0] == 1
assert sector_model.column_labels[0] == model.column_labels[m]
def test_make_featuremat(example_data):
model = DataModel(example_data)
assert model is not None
model.make()
featuremat_model = FeaturematModel(model)
featuremat_model.make()
def _build_model(self, filename, *args, **kwargs):
try:
model = DataModel(filename)
model.make()
return model
except Exception:
self._load_error()
return None
def test_single_sector_subtree_experiments(example_data):
model = DataModel(example_data)
assert model is not None
model.make()
print(model.sector_mapping)
single_sector_model = SingleSectorDataModel(model, 1)
single_sector_model.make()
lmat = np.array(single_sector_model.lmat)
print(lmat[:, 0])
print(lmat[:, 1])
def model_fixture(example_data):
model = DataModel(example_data)
model.make()
return model
def main(argv=None):
if argv is None:
argv = sys.argv
else:
argv.extend(sys.argv)
program_name = os.path.basename(sys.argv[0])
program_shortdesc = "SCGV is an interacive graphical tool for " \
"single-cell genomics data, with emphasis on single-cell " \
"genomics of cancer"
program_description = '''%s
USAGE
''' % (program_shortdesc, )
program_version_message = "1.0.3"
try:
parser = ArgumentParser(description=program_description,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('-V',
'--version',
action='version',
version=program_version_message)
parser.add_argument('-d',
'--directory',
type=str,
dest='directory',
metavar='<dir name>',
help='load data from directory')
parser.add_argument(
'-o',
'--output',
type=str,
dest='output',
metavar='<output filename>',
help='saves main view in a figure with specified filename')
parser.add_argument('-t',
'--title',
type=str,
dest='title',
metavar='<figure title>',
help='adds title to the saved figure')
parser.add_argument('-r',
'--resolution',
type=int,
dest='resolution',
metavar='<resolution>',
help='figure output resolution',
default=300)
args = parser.parse_args()
print(args)
if args.directory is not None and args.output is not None:
assert os.path.exists(args.directory)
model = DataModel(args.directory)
model.make()
canvas = Canvas()
canvas.model = model
canvas.redraw()
if args.title is not None:
canvas.fig.suptitle(args.title, fontsize=24)
canvas.fig.savefig(args.output, dpi=args.resolution)
return 0
app = QApplication(sys.argv)
window = MainWindow()
window.show()
if args.directory is not None:
window.open_buttons.load_model(args.directory)
app.exec_()
return 0
except KeyboardInterrupt:
traceback.print_exc()
return 0
except Exception as e:
traceback.print_exc()
indent = len(program_name) * " "
sys.stderr.write(program_name + ": " + repr(e) + "\n")
sys.stderr.write(indent + " for help use --help")
sys.stderr.write('\n')
return 2