def test_plot_scatter() -> None:
"""
Test plot scatter function.
"""
demo_objects: DemoObjects = DemoObjects()
dict_objects: Dict[str, Screen] = {
"hras": demo_objects.hras_rbd,
"bla": demo_objects.bla
}
# Define aux function
def _test_plot_scatter(obj_test: Screen, parameters: list) -> bool:
try:
obj_test.scatter(
obj_test,
**parameters) # pass dictionary as arguments of method
except Exception as e: # pylint: disable=broad-except
logging.exception(e)
print(traceback.format_exc())
return True
return False
# Define dictionary of parameters
# Each dict in the list will be a different set of parameters
list_params: list = [
{
'show': False,
'close': True,
},
{
'figsize': (3, 2.5),
'y_label': r'$∆E^i_x$',
'show': False,
'close': True,
},
]
# Assert
for obj_label, obj_test in dict_objects.items(
): # Loop over the dictionary
for parameters in list_params: # Loop over the parameters
assert _test_plot_scatter( # Assert that that set of parameters works on that object
obj_test,
parameters,
) is False, "plot_scatter failed with {} object and {} parameters".format(
obj_label,
parameters,
)
def test_demo_objects() -> None:
"""
Test class DemoObjects.
"""
demo_object: DemoObjects = DemoObjects()
assert isinstance(demo_object.hras_rbd, Screen)
assert isinstance(demo_object.bla, Screen)
assert isinstance(demo_object.sumo, Screen)
assert isinstance(demo_object.mapk1, Screen)
assert isinstance(demo_object.ube2i, Screen)
assert isinstance(demo_object.tat, Screen)
assert isinstance(demo_object.rev, Screen)
assert isinstance(demo_object.asynuclein, Screen)
assert isinstance(demo_object.aph, Screen)
assert isinstance(demo_object.b11l5f, Screen)
assert isinstance(demo_object.hras_counts, Counts)
"""
This module will test the heatmap plotting methods.
"""
import traceback
import logging
from typing import List
from mutagenesis_visualization.main.demo.demo_objects import DemoObjects
DEMO_OBJECTS: DemoObjects = DemoObjects()
OBJ_TEST = DEMO_OBJECTS.hras_rbd
def test_heatmap() -> None:
"""
Test the heatmap plot method.
"""
def _test_heatmap_output(parameters: dict) -> bool:
try:
OBJ_TEST.heatmap(**parameters) # pass dictionary as arguments of method
except Exception as e: # pylint: disable=broad-except
logging.exception(e)
print(traceback.format_exc())
return True
return False
# Define dictionary of parameters
# Each dict in the list will be a different set of parameters
list_params: List[dict] = [
{'show': False, 'close': True},
{'mask_selfsubstitutions': True, 'hierarchical': True, 'show': False, 'close': True},
"""
In this module we will produce the figures that went into the paper.
"""
from typing import List, Tuple
import numpy as np
from mutagenesis_visualization.main.demo.demo_objects import DemoObjects
from mutagenesis_visualization.main.classes.screen import Screen
HRAS_RBD = DemoObjects().hras_rbd
HRAS_COUNTS = DemoObjects().hras_counts
PATH: str = "docs/images/exported_images/paper/fig1{}.png"
ANC_RAS_ENRICHMENT = np.genfromtxt(
"figures_jk/enrichments/old/Ancestral167_RBD.csv", delimiter=',')
SHOW = False
def create_anc_ras_object() -> Tuple[Screen, List[Tuple[int, int]]]:
"""
This dataset is not available since it is not published yet.
"""
ancras: str = 'MTEYKLVVVGGGGVGKSALTIQFIQSHFVDEYDPTIEDSYRKQVVIDDEVAILDILDTAGQEEYSAMREQYMRNGEGFLLVYSITDRSSFDEISTYHEQILRVKDTDDVPMVLVGNKADLESRAVSMQEGQNLAKQLNVPFIETSAKQRMNVDEAFYTLVRVVRRH'
hras: str = 'MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH'
secondary: list = [
['β1'] * (9 - 1), ['L1'] * (16 - 9), ['α1'] * (25 - 16), ['L2'] *
(37 - 25), ['β2'] * (46 - 37), ['L3'] * (49 - 46), ['β3'] * (58 - 49),
['L4'] * (65 - 58), ['α2'] * (74 - 65), ['L5'] * (77 - 74),
['β4'] * (83 - 77), ['L6'] * (87 - 83), ['α3'] * (103 - 87),
['L7'] * (111 - 103), ['β5'] * (116 - 111), ['L8'] * (127 - 116),
['α4'] * (137 - 127), ['L9'] * (141 - 137), ['β6'] * (143 - 141),
['L10'] * (152 - 143), ['α5'] * (173 - 152), ['L11'] * (189 - 173)
]