def test_bad_object(self):
# Iterable includes elements that are not ggplot objects
fn = next(filename_gen)
plots = list(p()) + ['foo']
with pytest.raises(TypeError):
save_as_pdf_pages(plots, fn)
assert_exist_and_clean(fn, "bad ggplot object")
def test_plot_exception(self):
# Force an error in drawing
fn = next(filename_gen)
plots = list(p())
plots[0] += aes(color='unknown')
with pytest.raises(PlotnineError):
save_as_pdf_pages(plots, fn)
assert_exist_and_clean(fn, "Plot exception")
def generate_pdf(pcoa_qza, metadata, file_name, output_dir, point_size=6):
"""
Generates a single pdf file with multiple PCoA plots
Input:
- pcoa_qza: PCoA QIIME2 Artifact
- metadata: path to metadata file
- file_name: name of the output file
- output_dir: directory to save output file in
- point_size: ggplot point size. Default=6
"""
pcoa = convert_qiime2_2_skbio(pcoa_qza)
#generate_pcoa_plot(pcoa, metadata_df, args.target_primary)
output_name = "PCoA_plots_all.pdf"
save_as_pdf_pages(run_multiple(pcoa, metadata, point_size),
filename=file_name,
path=output_dir)
def test_save_method(self):
fn = next(filename_gen)
with pytest.warns(UserWarning) as record:
save_as_pdf_pages(p(), fn)
assert_exist_and_clean(fn, "save method")
res = ('filename' in str(item.message).lower() for item in record)
assert any(res)
# verbose
fn = next(filename_gen)
with pytest.warns(None) as record:
save_as_pdf_pages(p(), fn, verbose=False)
assert_exist_and_clean(fn, "save method")
res = ('filename' in str(item.message).lower() for item in record)
assert not any(res)
data = {}
for column in cols:
filename = column + "." + image_format
data[column] = filename
with open(output_path, 'w') as fh:
json.dump(data, fh)
if __name__ == "__main__":
parser = args_parse()
# Print help messages if no arguments are supplied
if (len(sys.argv) < 2):
parser.print_help()
sys.exit(0)
args = parser.parse_args()
pcoa = convert_qiime2_2_skbio(args.pcoa_qza)
# Load metadata into pandas dataframe
metadata_df = load_metadata(args.metadata)
#generate_pcoa_plot(pcoa, metadata_df, args.target_primary)
output_name = "PCoA_plots_all.pdf"
save_as_pdf_pages(run_multiple(pcoa, args.metadata, args.point_size),
filename=args.file_name,
path=args.output_dir)
def test_height_width(self):
plots = []
for i, plot in enumerate(p()):
plots.append(plot + theme(figure_size=(8+i, 6+i)))
fn = next(filename_gen)
save_as_pdf_pages(plots, fn)
def test_filename_plot_path(self):
fn = next(filename_gen)
save_as_pdf_pages(p(), fn, path='.')
assert_exist_and_clean(fn, "fn, plot and path")
def test_default_filename(self):
plots = list(p())
save_as_pdf_pages(plots)
fn = plots[0]._save_filename('pdf')
assert_exist_and_clean(fn, "default filename")
def test_save_as_pdf_pages_closes_plots():
assert plt.get_fignums() == [], "There are unsaved test plots"
fn = next(filename_gen)
save_as_pdf_pages(p(), fn)
assert_exist_and_clean(fn, "exist")
assert plt.get_fignums() == [], "ggplot.save did not close the plot"
def test_plot_exception(self):
# Force an error in drawing
plots = list(p())
plots[0] += aes(color='unknown')
with pytest.raises(PlotnineError):
save_as_pdf_pages(plots)
def test_bad_object(self):
# Iterable includes elements that are not ggplot objects
plots = list(p()) + ['foo']
with pytest.raises(TypeError):
save_as_pdf_pages(plots)
