flapjack

Submodules

Package Contents

Classes

Flapjack

Simulator

Functions

exponential_growth(t, y0, k)

exponential_growth_rate(t, y0, k)

fit_curve(func, data, x, y, **kwargs)

gompertz(t, y0, ymax, um, l)

gompertz_growth_rate(t, y0, ymax, um, l)

hill(x, a, b, k, n)

layout_print(fig, width=3.3, height=1.5, font_size=6)

Layout figure optimized for print at 300dpi

Attributes

colors

index_params

plot_option_keys

replace_columns_with_ids

class Flapjack(url_base='localhost:8000')
models = ['study', 'assay', 'sample', 'strain', 'media', 'vector', 'dna', 'signal', 'chemical',...
__del__(self)
async _analysis(self, **kwargs)
async _measurements(self, **kwargs)
async _plot(self, **kwargs)
async _upload_measurements(self, df, **kwargs)
analysis(self, **kwargs)
create(self, model, confirm=True, overwrite=False, **kwargs)
delete(self, model, id, confirm=True)
get(self, model, **kwargs)
handle_response(self, s)
log_in(self, username, password)
log_out(self)
measurements(self, **kwargs)
parse_params(self, **kwargs)
patch(self, model, id, **kwargs)
plot(self, **kwargs)
refresh(self)
upload_measurements(self, df, **kwargs)
class Simulator(study_name='', assay_name='', study_description='', assay_description='', dna_name='', init_proteins=[0], concentrations=[0], n_signals=1, fluo_noise=0.01, od_noise=0.01)
create_data(self, fj, step, n_samples, nt, dt, sim_steps)
create_meta_objects(self, fj)
colors = ['red', 'green', 'blue']
exponential_growth(t, y0, k)
exponential_growth_rate(t, y0, k)
fit_curve(func, data, x, y, **kwargs)
gompertz(t, y0, ymax, um, l)
gompertz_growth_rate(t, y0, ymax, um, l)
hill(x, a, b, k, n)
index_params = ['biomass_signal', 'ref_signal', 'analyte', 'analyte1', 'analyte2']
layout_print(fig, width=3.3, height=1.5, font_size=6)

Layout figure optimized for print at 300dpi

fig = figure to layout width,height = size in inches font_size = font size in pts

Returns: fig = figure with correct layout

plot_option_keys = ['normalize', 'subplots', 'markers', 'plot']
replace_columns_with_ids = []