Error in Plotting validation summary in 0.52 version

[YubinXie]

The 0.52 version fixed most of bugs in simulated data, but the last one (aka Plotting validation summary) still has a bug as attached.

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-9-14f90d916de1> in <module>()
     14 ot_model = wot.ot.initialize_ot_model(matrix_file, days_file,
     15                                       covariate=covariate_file, growth_iters=1, tmap_prefix='val')
---> 16 vs = wot.commands.compute_validation_summary(ot_model)
     17 vs['time'] = (vs['interval_start'] + vs['interval_end']) / 2
     18 vs['type'] = vs['pair0'].astype(str).str[0]

~/.local/lib/python3.6/site-packages/wot/commands/optimal_transport_validation.py in compute_validation_summary(ot_model, day_pairs_triplets, save_interpolated, interp_size, compute_full_distances)
     55 
     56     if has_covariate:
---> 57         ot_model.compute_all_transport_maps(with_covariates=True)
     58     if compute_full_distances:
     59         ot_model.compute_all_transport_maps()

~/.local/lib/python3.6/site-packages/wot/ot/ot_model.py in compute_all_transport_maps(self, with_covariates)
    218         else:
    219             for x in day_pairs:
--> 220                 self.compute_transport_map(*x)
    221 
    222     def compute_transport_map(self, t0, t1, covariate=None):

~/.local/lib/python3.6/site-packages/wot/ot/ot_model.py in compute_transport_map(self, t0, t1, covariate)
    264 
    265         config = {**self.ot_config, **local_config, 't0': t0, 't1': t1, 'covariate': covariate}
--> 266         tmap = OTModel.compute_single_transport_map(self.matrix, config)
    267         if tmap is not None:
    268             wot.io.write_dataset(tmap, output_file, output_format=self.output_file_format)

~/.local/lib/python3.6/site-packages/wot/ot/ot_model.py in compute_single_transport_map(ds, config)
    341         delta_days = t1 - t0
    342         config['g'] = config['g'] ** delta_days
--> 343         tmap = wot.ot.transport_stable_learn_growth(C, **config)
    344         return anndata.AnnData(tmap, p0.obs.copy(), p1.obs.copy())

TypeError: transport_stable_learn_growth() got an unexpected keyword argument 'tmap_prefix'

[joshua-gould]

Thanks, I updated the documentation.

[geoffschieb]

Dear Yubin, We have just released a tutorial on real data: https://broadinstitute.github.io/wot/tutorial/ Best, Geoff

…

On Thu, Feb 21, 2019 at 7:00 PM Yubin ***@***.***> wrote: The 0.52 version fixed most of bugs in simulated data, but the last one still has a bug as attached. --------------------------------------------------------------------------- TypeError Traceback (most recent call last) <ipython-input-9-14f90d916de1> in <module>() 14 ot_model = wot.ot.initialize_ot_model(matrix_file, days_file, 15 covariate=covariate_file, growth_iters=1, tmap_prefix='val') ---> 16 vs = wot.commands.compute_validation_summary(ot_model) 17 vs['time'] = (vs['interval_start'] + vs['interval_end']) / 2 18 vs['type'] = vs['pair0'].astype(str).str[0] ~/.local/lib/python3.6/site-packages/wot/commands/optimal_transport_validation.py in compute_validation_summary(ot_model, day_pairs_triplets, save_interpolated, interp_size, compute_full_distances) 55 56 if has_covariate: ---> 57 ot_model.compute_all_transport_maps(with_covariates=True) 58 if compute_full_distances: 59 ot_model.compute_all_transport_maps() ~/.local/lib/python3.6/site-packages/wot/ot/ot_model.py in compute_all_transport_maps(self, with_covariates) 218 else: 219 for x in day_pairs: --> 220 self.compute_transport_map(*x) 221 222 def compute_transport_map(self, t0, t1, covariate=None): ~/.local/lib/python3.6/site-packages/wot/ot/ot_model.py in compute_transport_map(self, t0, t1, covariate) 264 265 config = {**self.ot_config, **local_config, 't0': t0, 't1': t1, 'covariate': covariate} --> 266 tmap = OTModel.compute_single_transport_map(self.matrix, config) 267 if tmap is not None: 268 wot.io.write_dataset(tmap, output_file, output_format=self.output_file_format) ~/.local/lib/python3.6/site-packages/wot/ot/ot_model.py in compute_single_transport_map(ds, config) 341 delta_days = t1 - t0 342 config['g'] = config['g'] ** delta_days --> 343 tmap = wot.ot.transport_stable_learn_growth(C, **config) 344 return anndata.AnnData(tmap, p0.obs.copy(), p1.obs.copy()) TypeError: transport_stable_learn_growth() got an unexpected keyword argument 'tmap_prefix' — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#34>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AJIoYgjz9S4PdBpHnW01QCF3lpqFmxzFks5vPzMVgaJpZM4bIlEs> .

[YubinXie]

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