def test_Logo_style_xticks():
good_crp_df = logomaker.get_example_matrix('crp_energy_matrix',
print_description=False)
# test parameter anchor
test_parameter_values(func=logomaker.Logo(good_crp_df).style_xticks,
var_name='anchor',
fail_list=['x', None, 0.5, 1.0],
success_list=[-1, 1, 2])
# test parameter spacing
test_parameter_values(func=logomaker.Logo(good_crp_df).style_xticks,
var_name='spacing',
fail_list=['x', None, 0, 0.5],
success_list=[1, 2])
# test parameter fmt
# TODO: fmt = 'x' seems to passing in the following. This should be fixed.
test_parameter_values(func=logomaker.Logo(good_crp_df).style_xticks,
var_name='fmt',
fail_list=[None, 0],
success_list=['%d'])
# test parameter rotation
test_parameter_values(func=logomaker.Logo(good_crp_df).style_xticks,
var_name='rotation',
fail_list=[None, 'x'],
success_list=[-12, 0, 1.4, 200])
def test_Logo_style_glyphs_below():
good_crp_df = logomaker.get_example_matrix('crp_energy_matrix',
print_description=False)
# test parameter color
test_parameter_values(
func=logomaker.Logo(good_crp_df).style_glyphs_below,
var_name='color',
fail_list=[0, 'xxx', True, [0, 0, -1]],
success_list=['red', [1, 1, 1], [0, 0, 0], [0.1, 0.2, 0.3], None])
# test parameter alpha
test_parameter_values(func=logomaker.Logo(good_crp_df).style_glyphs_below,
var_name='alpha',
fail_list=[-1, 'x', 1.1],
success_list=[0, 1, 0.5])
# test parameter shade
test_parameter_values(func=logomaker.Logo(good_crp_df).style_glyphs_below,
var_name='shade',
fail_list=[-1, 'x', 1.1],
success_list=[0, 1, 0.5])
# test parameter fade
test_parameter_values(func=logomaker.Logo(good_crp_df).style_glyphs_below,
var_name='fade',
fail_list=[-1, 'x', 1.1],
success_list=[0, 1, 0.5])
# test parameter flip
test_parameter_values(func=logomaker.Logo(good_crp_df).style_glyphs_below,
var_name='flip',
fail_list=bool_fail_list,
success_list=bool_success_list)
def test_Logo_highlight_position():
good_crp_df = logomaker.get_example_matrix('crp_energy_matrix',
print_description=False)
# test parameter p
test_parameter_values(func=logomaker.Logo(good_crp_df).highlight_position,
var_name='p',
fail_list=['x', 1.5],
success_list=[0, 1, 10])
def test_Logo_style_glyphs():
good_crp_df = logomaker.get_example_matrix('crp_energy_matrix',
print_description=False)
# test parameter color_scheme
test_parameter_values(func=logomaker.Logo(good_crp_df).style_glyphs,
var_name='color_scheme',
fail_list=['bad_color_scheme', 1, True],
success_list=['classic', 'gray', 'salmon'])
def test_Logo_style_single_glyph():
good_crp_df = logomaker.get_example_matrix('crp_energy_matrix',
print_description=False)
# test parameter p
test_parameter_values(func=logomaker.Logo(good_crp_df).style_single_glyph,
var_name='p',
fail_list=[-1, 'x', 1.1, 10000],
success_list=[0, 1, 10],
c='A')
# test parameter c
test_parameter_values(func=logomaker.Logo(good_crp_df).style_single_glyph,
var_name='c',
fail_list=[-1, 'x', 1.1],
success_list=['A', 'C', 'G', 'T'],
p=1)
def test_Logo_fade_glyphs_in_probability_logo():
good_prob_df = logomaker.get_example_matrix('ss_probability_matrix',
print_description=False)
# test parameter v_alpha0
test_parameter_values(
func=logomaker.Logo(good_prob_df).fade_glyphs_in_probability_logo,
var_name='v_alpha0',
fail_list=[-1, 1.1, 1, 1.0, 'xxx', True],
success_list=[0, 0.0, 0.999, 0.5])
# TODO: a value of True v_alpha_1 works now, this should probably be fixed.
# test parameter v_alpha1
test_parameter_values(
func=logomaker.Logo(good_prob_df).fade_glyphs_in_probability_logo,
var_name='v_alpha1',
fail_list=[1.1, -1, 'xxx'],
success_list=[0.999, 0.5, 1.0])
def test_Logo_draw_baseline():
good_crp_df = logomaker.get_example_matrix('crp_energy_matrix',
print_description=False)
# test parameter zorder
test_parameter_values(func=logomaker.Logo(good_crp_df).draw_baseline,
var_name='zorder',
fail_list=['x', None],
success_list=[-1, 0.5, 1])
# test parameter color
test_parameter_values(func=logomaker.Logo(good_crp_df).draw_baseline,
var_name='color',
fail_list=['x', 1, True, 'wrong_color'],
success_list=['pink', 'red', [1, 1, 1]])
# test parameter linewidth
test_parameter_values(func=logomaker.Logo(good_crp_df).draw_baseline,
var_name='linewidth',
fail_list=['x', -1, '1', None],
success_list=[0, 1, 1.5, 2])
def test_Logo_style_glyphs_in_sequence():
good_crp_df = logomaker.get_example_matrix('crp_energy_matrix',
print_description=False)
# randomly make up a sequence of the correct length
test_good_sequence = np.random.choice(['A', 'C', 'G', 'T'],
size=26,
p=[0.25, 0.25, 0.25, 0.25])
test_good_sequence = "".join(test_good_sequence)
# randomly make up a sequence of the incorrect length
test_bad_sequence = np.random.choice(['A', 'C', 'G', 'T'],
size=10,
p=[0.25, 0.25, 0.25, 0.25])
test_bad_sequence = "".join(test_bad_sequence)
# test parameter sequence
test_parameter_values(
func=logomaker.Logo(good_crp_df).style_glyphs_in_sequence,
var_name='sequence',
fail_list=[-1, 'x', 1.1, test_bad_sequence],
success_list=[test_good_sequence])
def test_Logo_style_spines():
good_crp_df = logomaker.get_example_matrix('crp_energy_matrix',
print_description=False)
# test parameter anchor
test_parameter_values(func=logomaker.Logo(good_crp_df).style_spines,
var_name='spines',
fail_list=['x', None, 0.5, 1.0, 'top'],
success_list=[('top', 'bottom', 'left', 'right'),
['top', 'bottom', 'left', 'right'],
('top', 'bottom', 'left'),
('top', 'bottom'), ['top']])
# test parameter visible
test_parameter_values(func=logomaker.Logo(good_crp_df).style_spines,
var_name='visible',
fail_list=bool_fail_list,
success_list=bool_success_list)
# test parameter color
test_parameter_values(func=logomaker.Logo(good_crp_df).style_spines,
var_name='color',
fail_list=['wrong_color', 3, [0.5, 0.5, 0.5, 0.5]],
success_list=['black', 'green', [0.4, 0.5, 1.0]])
# test parameter linewidth
test_parameter_values(func=logomaker.Logo(good_crp_df).style_spines,
var_name='linewidth',
fail_list=['xxx', -1],
success_list=[0.0, 0, 1])
# test parameter bounds
test_parameter_values(func=logomaker.Logo(good_crp_df).style_spines,
var_name='bounds',
fail_list=['xxx', -1],
success_list=[None, [0, 1]])
def test_transform_matrix():
good_crp_weight_df = logomaker.get_example_matrix('crp_energy_matrix',
print_description=False)
good_crp_counts_df = logomaker.get_example_matrix('crp_counts_matrix',
print_description=False)
# test parameter df
test_parameter_values(func=logomaker.transform_matrix,
var_name='df',
fail_list=['x', good_crp_weight_df, None],
success_list=[good_crp_counts_df],
from_type='counts',
to_type='probability')
test_parameter_values(func=logomaker.transform_matrix,
var_name='df',
fail_list=[],
success_list=[good_crp_counts_df],
from_type='counts',
to_type='weight')
test_parameter_values(func=logomaker.transform_matrix,
var_name='df',
fail_list=[],
success_list=[good_crp_counts_df],
from_type='counts',
to_type='information')
# test parameter center_values
test_parameter_values(func=logomaker.transform_matrix,
var_name='center_values',
fail_list=bool_fail_list,
success_list=bool_success_list,
df=good_crp_counts_df)
# test parameter normalize_values
test_parameter_values(func=logomaker.transform_matrix,
var_name='normalize_values',
fail_list=bool_fail_list,
success_list=bool_success_list,
df=good_crp_counts_df)
# test parameter from_type
test_parameter_values(func=logomaker.transform_matrix,
var_name='from_type',
fail_list=[1, 'x', None],
success_list=['counts'],
df=good_crp_counts_df,
to_type='probability')
# test parameter to_type
test_parameter_values(
func=logomaker.transform_matrix,
var_name='to_type',
fail_list=[1, 'x', None],
success_list=['probability', 'weight', 'information'],
df=good_crp_counts_df,
from_type='counts')
# test parameter background
test_parameter_values(func=logomaker.transform_matrix,
var_name='background',
fail_list=[1, 'x', [-1, 1, 1, 1]],
success_list=[None, [0.25, 0.25, 0.25, 0.25]],
df=good_crp_counts_df,
from_type='counts',
to_type='information')
# test parameter pseudocount
test_parameter_values(func=logomaker.transform_matrix,
var_name='pseudocount',
fail_list=[None, 'x', -1],
success_list=[0, 1, 10],
df=good_crp_counts_df,
from_type='counts',
to_type='probability')
def test_Logo_highlight_position_range():
good_crp_df = logomaker.get_example_matrix('crp_energy_matrix',
print_description=False)
# test parameter pmin
test_parameter_values(
func=logomaker.Logo(good_crp_df).highlight_position_range,
var_name='pmin',
fail_list=['x', 20],
success_list=[0, 1, 10],
pmax=15)
# test parameter pmax
test_parameter_values(
func=logomaker.Logo(good_crp_df).highlight_position_range,
var_name='pmax',
fail_list=['x', 1],
success_list=[5.5, 6, 10],
pmin=5)
# test parameter padding
test_parameter_values(
func=logomaker.Logo(good_crp_df).highlight_position_range,
var_name='padding',
fail_list=['x', -1],
success_list=[-0.5, 0, 10],
pmin=5,
pmax=10)
# test parameter color
test_parameter_values(
func=logomaker.Logo(good_crp_df).highlight_position_range,
var_name='color',
fail_list=['x', 1, True, 'wrong_color'],
success_list=['pink', 'red', [1, 1, 1]],
pmin=5,
pmax=10)
# test parameter edgecolor
test_parameter_values(
func=logomaker.Logo(good_crp_df).highlight_position_range,
var_name='edgecolor',
fail_list=['x', 1, True, 'wrong_color'],
success_list=[None, 'pink', 'red', [1, 1, 1]],
pmin=5,
pmax=10)
# test parameter floor
test_parameter_values(
func=logomaker.Logo(good_crp_df).highlight_position_range,
var_name='floor',
fail_list=['x', 10],
success_list=[-1, 1, None],
pmin=5,
pmax=10)
# test parameter ceiling
test_parameter_values(
func=logomaker.Logo(good_crp_df).highlight_position_range,
var_name='ceiling',
fail_list=['x', -10],
success_list=[-1, 1, None],
pmin=5,
pmax=10)
# test parameter zorder. Note that a value of False passes for this parameter. This should be fixed.
test_parameter_values(
func=logomaker.Logo(good_crp_df).highlight_position_range,
var_name='zorder',
fail_list=['x', None],
success_list=[-1, 0.5, 1],
pmin=5,
pmax=10)
# do imports
import matplotlib.pyplot as plt
import numpy as np
import logomaker as logomaker
# load saliency matrix
nn_df = logomaker.get_example_matrix('nn_saliency_matrix',
print_description=False)
# create Logo object
nn_logo = logomaker.Logo(nn_df)
# style using Logo methods
nn_logo.style_spines(visible=False)
nn_logo.style_spines(spines=['left'], visible=True, bounds=[0, .75])
# style using Axes methods
nn_logo.ax.set_xlim([20, 115])
nn_logo.ax.set_xticks([])
nn_logo.ax.set_ylim([-.6, .75])
nn_logo.ax.set_yticks([0, .75])
nn_logo.ax.set_yticklabels(['0', '0.75'])
nn_logo.ax.set_ylabel(' saliency', labelpad=-1)
# set parameters for drawing gene
exon_start = 55 - .5
exon_stop = 90 + .5
y = -.2
xs = np.arange(-3, len(nn_df), 10)
ys = y * np.ones(len(xs))
def test_Logo():
# df inputs that successfully execute when entered into Logo.
good_crp_df = logomaker.get_example_matrix('crp_energy_matrix',
print_description=False)
good_prob_df = logomaker.get_example_matrix('ss_probability_matrix',
print_description=False)
random_df = pd.DataFrame(np.random.randint(0, 3, size=(10, 4)),
columns=list('ACGT'))
# df inputs that fail when entered into Logo.
bad_df1 = 'x'
# test parameter df
test_parameter_values(func=logomaker.Logo,
var_name='df',
fail_list=[bool_fail_list, bad_df1],
success_list=[good_crp_df, random_df])
# test parameter colors
test_parameter_values(
func=logomaker.Logo,
var_name='color_scheme',
fail_list=['x', 'bad_color_name', 3],
success_list=['classic', 'grays', 'charge', 'salmon'],
df=good_crp_df)
# test parameter font names
test_parameter_values(func=logomaker.Logo,
var_name='font_name',
fail_list=[True, None, good_crp_df],
success_list=[
'DejaVu Sans', 'Arial Rounded MT Bold',
'Times New Roman'
],
df=good_crp_df)
# test parameter stack_order
test_parameter_values(func=logomaker.Logo,
var_name='stack_order',
fail_list=['incorrect argument', 0.0, None],
success_list=['small_on_top', 'big_on_top', 'fixed'],
df=good_crp_df)
# test parameter center_values
test_parameter_values(func=logomaker.Logo,
var_name='center_values',
fail_list=['incorrect argument', 0.0, None],
success_list=[True, False],
df=good_crp_df)
# test parameter baseline_width
test_parameter_values(func=logomaker.Logo,
var_name='baseline_width',
fail_list=['incorrect argument', -0.1, None],
success_list=[0, 0.5, 3],
df=good_crp_df)
# test parameter flip_below
test_parameter_values(func=logomaker.Logo,
var_name='flip_below',
fail_list=['incorrect argument', -0.1, None],
success_list=[True, False],
df=good_crp_df)
# test parameter shade_below
test_parameter_values(func=logomaker.Logo,
var_name='shade_below',
fail_list=['incorrect argument', -0.1, 1.4, None],
success_list=[0, 0.0, 0.5, 1, 1.0],
df=good_crp_df)
# test parameter fade_below
test_parameter_values(func=logomaker.Logo,
var_name='fade_below',
fail_list=['incorrect argument', -0.1, 1.4, None],
success_list=[0, 0.0, 0.5, 1, 1.0],
df=good_crp_df)
# test parameter fade_probabilities
test_parameter_values(func=logomaker.Logo,
var_name='fade_probabilities',
fail_list=['incorrect argument', -0.1, 1.4, None],
success_list=[True, False],
df=good_prob_df)
# test parameter vsep
test_parameter_values(func=logomaker.Logo,
var_name='vsep',
fail_list=['incorrect argument', -0.1, None],
success_list=[0.0, 0, 0.3, 10],
df=good_crp_df)
# test parameter vsep
# TODO: note that a value of True/False is still causing a logo to be drawn, eventhough draw_now = False
test_parameter_values(func=logomaker.Logo,
var_name='show_spines',
fail_list=['incorrect argument', -0.1],
success_list=[None, True, False],
df=good_crp_df)
# test parameter zorder. Need to review zorder's input check in Logo
test_parameter_values(func=logomaker.Logo,
var_name='zorder',
fail_list=['incorrect argument'],
success_list=[0, 1, 3],
df=good_crp_df)
# test parameter figsize
test_parameter_values(func=logomaker.Logo,
var_name='figsize',
fail_list=[
'incorrect argument', -0.1, [-1, -1], [-1],
[0, 0], ['x', 'y'], (1, 2, 3)
],
success_list=[(10, 2.5), [5, 5]],
df=good_crp_df)
# validate ax
_, temp_ax = plt.subplots(figsize=[3, 3])
test_parameter_values(func=logomaker.Logo,
var_name='ax',
fail_list=['x', 1, True],
success_list=[temp_ax, None],
df=good_crp_df)
# do imports
import matplotlib.pyplot as plt
import logomaker as logomaker
# load ww information matrix
ww_df = logomaker.get_example_matrix('ww_information_matrix',
print_description=False)
# create Logo object
ww_logo = logomaker.Logo(ww_df,
font_name='Stencil Std',
color_scheme='NajafabadiEtAl2017',
vpad=.1,
width=.8)
# style using Logo methods
ww_logo.style_xticks(anchor=0, spacing=5, rotation=45)
ww_logo.highlight_position(p=4, color='gold', alpha=.5)
ww_logo.highlight_position(p=26, color='gold', alpha=.5)
# style using Axes methods
ww_logo.ax.set_ylabel('information (bits)')
ww_logo.ax.set_xlim([-1, len(ww_df)])
# show plot
ww_logo.fig.show()
# do imports
import matplotlib.pyplot as plt
import logomaker as logomaker
# load crp energy matrix
crp_df = -logomaker.get_example_matrix('crp_energy_matrix',
print_description=False)
# create Logo object
crp_logo = logomaker.Logo(crp_df,
shade_below=.5,
fade_below=.5,
font_name='Arial Rounded MT Bold')
# style using Logo methods
crp_logo.style_spines(visible=False)
crp_logo.style_spines(spines=['left', 'bottom'], visible=True)
crp_logo.style_xticks(rotation=90, fmt='%d', anchor=0)
# style using Axes methods
crp_logo.ax.set_ylabel("$-\Delta \Delta G$ (kcal/mol)", labelpad=-1)
crp_logo.ax.xaxis.set_ticks_position('none')
crp_logo.ax.xaxis.set_tick_params(pad=-1)
# style and show figure
crp_logo.fig.show()
# do imports
import matplotlib.pyplot as plt
import logomaker as logomaker
# load ss probability matrix
ss_df = logomaker.get_example_matrix('ss_probability_matrix',
print_description=False)
# create Logo object
ss_logo = logomaker.Logo(ss_df,
width=.8,
vpad=.05,
fade_probabilities=True,
stack_order='small_on_top',
color_scheme='dodgerblue',
font_name='Rosewood Std')
# style using Logo methods
ss_logo.style_spines(spines=['left', 'right'], visible=False)
# style using Axes methods
ss_logo.ax.set_xticks(range(len(ss_df)))
ss_logo.ax.set_xticklabels('%+d'%x for x in [-3, -2, -1, 1, 2, 3, 4, 5, 6])
ss_logo.ax.set_yticks([0, .5, 1])
ss_logo.ax.axvline(2.5, color='k', linewidth=1, linestyle=':')
ss_logo.ax.set_ylabel('probability')
# show plot
ss_logo.fig.show()
# do imports
import matplotlib.pyplot as plt
import logomaker as logomaker
# make Figure and Axes objects
fig, ax = plt.subplots(1, 1, figsize=[4, 2])
# load logo matrix
logo_df = logomaker.get_example_matrix('logomaker_logo_matrix',
print_description=False)
# create color scheme
color_scheme = {
'L': [0, .5, 0],
'O': [1, 0, 0],
'G': [1, .65, 0],
'maker': 'gray'
}
# create Logo object
logo_logo = logomaker.Logo(logo_df,
ax=ax,
color_scheme=color_scheme,
baseline_width=0,
font_name='Arial',
show_spines=False,
vsep=.005,
width=.95)
# color the 'O' at the end of the logo a different color
logo_logo.style_single_glyph(c='O', p=3, color=[0, 0, 1])
# do imports
import matplotlib.pyplot as plt
import logomaker as logomaker
# load ARS enrichment matrix
ars_df = logomaker.get_example_matrix('ars_enrichment_matrix',
print_description=False)
# load wild-type ARS1 sequence
with logomaker.open_example_datafile('ars_wt_sequence.txt',
print_description=False) as f:
lines = f.readlines()
lines = [l.strip() for l in lines if '#' not in l]
ars_seq = ''.join(lines)
# trim matrix and sequence
start = 10
stop = 100
ars_df = ars_df.iloc[start:stop, :]
ars_df.reset_index(inplace=True, drop=True)
ars_seq = ars_seq[start:stop]
# create Logo object
ars_logo = logomaker.Logo(ars_df,
color_scheme='dimgray',
font_name='Luxi Mono')
# color wild-type ARS1 sequence within logo
ars_logo.style_glyphs_in_sequence(sequence=ars_seq, color='darkorange')
# highlight functional regions of ARS1
