My personal python library.
pip install dohlee
Plotting library. Provides simple ways to produce publication-ready plots.
dohlee.plot.mutation_signature
import dohlee.plot as plot; plot.set_style() # Sets plot styles.
ax = plot.get_axis(figsize=(20.4, 3.4))
plot.mutation_signature(data, ax=ax)
dohlee.plot.boxplot
ax = plot.get_axis(preset='wide', transpose=True)
plot.boxplot(data=iris, x='species', y='sepal_length', ax=ax)
dohlee.plot.histogram
ax = plot.get_axis(preset='wide')
plot.histogram(iris.sepal_length, bins=22, xlabel='Sepal Length', ylabel='Frequency', ax=ax)
dohlee.plot.frequency
ax = plot.get_axis(preset='wide')
plot.frequency(data, ax=ax, xlabel='Your numbers', ylabel='Frequency')
dohlee.plot.tsne
ax = plot.get_axis(preset='wide')
plot.tsne(
iris[['sepal_length', 'sepal_width', 'petal_length', 'petal_width']],
ax=ax,
s=5,
labels=iris['species']
)
dohlee.plot.stacked_bar_chart
# Generate sample data.
n_samples = 100
sample_dict = {'Sample': ['S%d' % i for i in range(1, n_samples + 1)]}
value_dict = {c: np.random.randint(0, 100, size=n_samples) for c in ['Missense', 'Nonsense', 'Silent']}
test_data = pd.DataFrame({**sample_dict, **value_dict})
# Plot stacked bar chart.
plot.stacked_bar_chart(
data=test_data,
x='Sample',
y=['Missense', 'Nonsense', 'Silent'],
ax=plot.get_axis(figsize=(14.4, 3.4)),
xticklabels=False,
sort=True,
ylabel='Number of mutations',
xlabel='Sample',
legend_size='xx-large')
dohlee.plot.linear_regression
ax = plot.get_axis(preset='wide')
x = np.linspace(0, 1, 100)
y = 2 * x + 3 + np.random.normal(0, 0.3, len(x))
plot.linear_regression(x, y, ax=ax)
Since this package is updated as needed when I'm doing my research, the development process fits well with TDD cycle.
- When you feel a need to write frequently-used research workflow as a function, write rough tests so that you can be sure that the function you've implemented just meets your need. Write the name of test function as verbose as possible!
- Run test with following commands. By default, nosetests ignores runnable files while finding test scripts. --exe option revokes it.
nosetests --exe --with-coverage --cover-package=dohleeOR
tox -e py35,py36- When sufficient progress have been made, test if the package can be published.
tox- If all tests are passed, distribute the package via PyPI.
python setup.py sdist
twine upload dist/dohlee-x.x.x.tar.gz