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clapy's Issues

Random seeds for the paper

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?

Remove simulator

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.

Update README.md

  • make clear that this is only about analysis, not simulation
  • add all dependencies: clasim cython iminuit matplotlib numpy pandas pytables scipy seaborn. Anything else?
  • describe the files in the repository
  • add our biorxiv under How to cite (copy-paste from clasim)

Creating figure 4.pdf does not work properly.

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:

And one of the plots is missing:
image

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