fbnrst / clapy Goto Github PK
View Code? Open in Web Editor NEWProliferation rate estimation from continuous labeling assays
License: Other
Proliferation rate estimation from continuous labeling assays
License: Other
Currently, we use randomized random seeds in paper_plots.ipynb
: seed=int(np.random.rand()*1000)
. This makes exact reproducibility impossible. Could we simply iterate over random seeds instead?
We decided to split the code between simulator and the parameter estimation. This repository should only contain the parameter estimation, so we need to remove the simulator part from here.
clasim cython iminuit matplotlib numpy pandas pytables scipy seaborn
. Anything else?It should also mention Nowakowski. Formatting should be done in scipy style.
I tried to run paper_plots.ipynb
. When executing the last cell, I get the following output:
['/minuit_full_newT_s100_GF095_m5', '/minuit_full_newT_s5_GF095_m5', '/minuit_full_t001_15_s100_GF095_m100', '/minuit_full_t001_15_s5_GF095_m5']
Tc not found
r not found
ss not found
sc not found
GFf not found
Tc not found
r not found
ss not found
sc not found
GFf not found
/home/fabrost/pksCloud/projects/continuous_labelling_assays/source/clapy/clapy.py:258: UserWarning: DataFrame has more than 2 dimension. Average is plotted
warnings.warn("DataFrame has more than 2 dimension. Average is plotted")
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-10-bed3945ea5bc> in <module>
210 cbar = plt.colorbar(im,ax=ax_12)
211 tl = cbar.ax.get_yticklabels()
--> 212 tl = [float(i.get_text()[1:-1]) for i in tl]
213 cbar.ax.set_yticklabels(['{:2.0f}'.format( (i-1)*100 )+"\%" for i in tl])
214
<ipython-input-10-bed3945ea5bc> in <listcomp>(.0)
210 cbar = plt.colorbar(im,ax=ax_12)
211 tl = cbar.ax.get_yticklabels()
--> 212 tl = [float(i.get_text()[1:-1]) for i in tl]
213 cbar.ax.set_yticklabels(['{:2.0f}'.format( (i-1)*100 )+"\%" for i in tl])
214
ValueError: could not convert string to float:
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