def dot_plot_results(means: str, pvalues: str, rows: str, columns: str, job_id: str):
with tempfile.TemporaryDirectory() as output_path:
with tempfile.NamedTemporaryFile(suffix=os.path.splitext(means)[-1]) as means_file:
with tempfile.NamedTemporaryFile(suffix=os.path.splitext(pvalues)[-1]) as pvalues_file:
with tempfile.NamedTemporaryFile() as rows_file:
with tempfile.NamedTemporaryFile() as columns_file:
_from_s3_to_temp(means, means_file)
_from_s3_to_temp(pvalues, pvalues_file)
_from_s3_to_temp(rows, rows_file)
_from_s3_to_temp(columns, columns_file)
output_name = 'plot__{}.png'.format(job_id)
dot_plot(means_file.name, pvalues_file.name, output_path, output_name, rows_file.name,
columns_file.name)
output_file = os.path.join(output_path, output_name)
if not os.path.exists(output_file):
raise PlotException('Could not generate output file for plot of type dot_plot')
response = {
'job_id': job_id,
'files': {
'plot': output_name,
},
'success': True
}
write_image_to_s3(output_file, output_name)
return response
def test_dot_plot_with_all_columns_and_rows(self):
means_path = self._get_input_file_path_for('means')
pvalues_path = self._get_input_file_path_for('pvalues')
plot_output = 'dot_plot_output_all_rows_columns.png'
dot_plot(means_path=means_path,
pvalues_path=pvalues_path,
output_path=output_test_dir,
output_name=plot_output
)
output_path = os.path.join(output_test_dir, plot_output)
self.assertTrue(os.path.exists(output_path), 'Plot of type dot_plot did not work')
self.assertGreater(os.path.getsize(output_path), 0)
os.remove(output_path)
def dot_plot(means_path: str, pvalues_path: str, output_path: str, output_name: str, rows: str,
columns: str, verbose: bool):
try:
r_plotter.dot_plot(means_path, pvalues_path, output_path, output_name, rows, columns)
except MissingR:
print('You cannot perform this plot command unless there is a working R setup according to CellPhoneDB specs')
except RRuntimeException as e:
app_logger.error(str(e))
except:
app_logger.error('Unexpected error')
if verbose:
traceback.print_exc(file=sys.stdout)
else:
app_logger.error('execute with --verbose to see full stack trace')