def heatmaps_plot_results(meta: str, pvalues: str, job_id: str):
with tempfile.TemporaryDirectory() as output_path:
with tempfile.NamedTemporaryFile(suffix=os.path.splitext(pvalues)[-1]) as pvalues_file:
with tempfile.NamedTemporaryFile() as meta_file:
_from_s3_to_temp(pvalues, pvalues_file)
_from_s3_to_temp(meta, meta_file)
count_name = 'plot_count__{}.png'.format(job_id)
count_log_name = 'plot_count_log__{}.png'.format(job_id)
heatmaps_plot(meta_file.name, pvalues_file.name, output_path, count_name, count_log_name)
output_count_file = os.path.join(output_path, count_name)
output_count_log_file = os.path.join(output_path, count_log_name)
if not os.path.exists(output_count_file) or not os.path.exists(output_count_log_file):
raise PlotException('Could not generate output file for plot of type dot_plot')
response = {
'job_id': job_id,
'files': {
'count_plot': count_name,
'count_log_plot': count_log_name
},
'success': True
}
write_image_to_s3(output_count_file, count_name)
write_image_to_s3(output_count_log_file, count_log_name)
return response
def heatmap_plot(meta_path: str, pvalues_path: str, output_path: str, count_name: str, log_name: str, verbose: bool):
try:
r_plotter.heatmaps_plot(meta_path, pvalues_path, output_path, log_name, count_name)
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')
def test_heatmaps_plot(self):
meta_path = self._get_fixture('hi_test_meta.txt')
pvalues_path = self._get_input_file_path_for('pvalues')
plot_output_counts = 'heatmaps_plot_counts.png'
plot_output_count_logs = 'heatmaps_plot_count_logs.png'
heatmaps_plot(meta_file=meta_path,
pvalues_file=pvalues_path,
output_path=output_test_dir,
count_name=plot_output_counts,
log_name=plot_output_count_logs,
pvalue=0.05)
for file in [plot_output_counts, plot_output_count_logs]:
output_path = os.path.join(output_test_dir, file)
self.assertTrue(os.path.exists(output_path),
'Plot of type heatmap_plot did not work')
self.assertGreater(os.path.getsize(output_path), 0)
os.remove(output_path)