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theislab / cellrank

CellRank: dynamics from multi-view single-cell data
https://cellrank.org
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Failed model: genes not translating to the model in .gene_trends #838

Closed keithgmitchell closed 2 years ago

keithgmitchell commented 2 years ago

...

model = cr.ul.models.GAM(adata)
cr.pl.gene_trends(
    adata,
    model,
    test_sig[0:20],
    ncols=3,
    data_key="Ms",
    color='pterotyping_donor__anno',
    time_key="ct_pseudotime",
    same_plot=True,
    figsize=(15, 4),
    n_test_points=200,
)
TypeError: Fatal model failure `<FailedModel[origin=GAM[gene=None, lineage=None, model=GammaGAM(callbacks=['deviance', 'diffs'], fit_intercept=True, max_iter=2000, scale=None, terms=s(0), tol=0.0001, verbose=False)]]>`.

Versions:

Package Version Location

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adjustText 0.7.3
aiohttp 3.8.1
aiosignal 1.2.0
airr 1.3.1
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cellrank 1.5.1
cellxgene 1.0.0
certifi 2019.11.28
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...

michalk8 commented 2 years ago

Hi @keithgmitchell , could you please post the full traceback? It contains the information needed for debugging.

keithgmitchell commented 2 years ago 
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
/usr/local/lib/python3.8/dist-packages/cellrank/ul/models/_base_model.py in wrapper(wrapped, instance, args, kwargs)
     64                     instance.reraise()
---> 65                 return wrapped(*args, **kwargs)
     66             except Exception as e:  # noqa: B902

TypeError: prepare() got an unexpected keyword argument 'color'

The above exception was the direct cause of the following exception:

TypeError                                 Traceback (most recent call last)
/tmp/ipykernel_347/1362536770.py in <module>
----> 1 velocygraphtor(annotated_final)

/tmp/ipykernel_347/797497014.py in velocygraphtor(annotated_final)
     75         # )
     76 
---> 77         cr.pl.gene_trends(
     78             adata,
     79             model,

/usr/local/lib/python3.8/dist-packages/cellrank/ul/_utils.py in _genesymbols(wrapped, instance, args, kwargs)
    284         use_raw=kwargs.get("use_raw", False),
    285     ):
--> 286         return wrapped(*args, **kwargs)

/usr/local/lib/python3.8/dist-packages/cellrank/pl/_gene_trend.py in gene_trends(adata, model, genes, lineages, backward, data_key, time_key, time_range, transpose, callback, conf_int, same_plot, hide_cells, perc, lineage_cmap, abs_prob_cmap, cell_color, cell_alpha, lineage_alpha, size, lw, cbar, margins, sharex, sharey, gene_as_title, legend_loc, obs_legend_loc, ncols, suptitle, return_models, n_jobs, backend, show_progress_bar, figsize, dpi, save, plot_kwargs, **kwargs)
    197     models = _create_models(model, genes, lineages)
    198 
--> 199     all_models, models, genes, lineages = _fit_bulk(
    200         models,
    201         _create_callbacks(adata, callback, genes, lineages, **kwargs),

/usr/local/lib/python3.8/dist-packages/cellrank/pl/_utils.py in _fit_bulk(models, callbacks, genes, lineages, time_range, parallel_kwargs, return_models, filter_all_failed, **kwargs)
    483     logg.info("    Finish", time=start)
    484 
--> 485     return _filter_models(
    486         models, return_models=return_models, filter_all_failed=filter_all_failed
    487     )

/usr/local/lib/python3.8/dist-packages/cellrank/pl/_utils.py in _filter_models(models, return_models, filter_all_failed)
    532                     model, FailedModel
    533                 ), f"Expected `FailedModel`, found `{type(model).__name__!r}`."
--> 534                 model.reraise()
    535 
    536     if not np.all(modelmask.values):

/usr/local/lib/python3.8/dist-packages/cellrank/ul/models/_base_model.py in reraise(self)
   1349         """Raise the original exception with additional model information."""
   1350         # retain the exception type and also the original exception
-> 1351         raise type(self._exc)(f"Fatal model failure `{self}`.") from self._exc
   1352 
   1353     def _get_colors(

TypeError: Fatal model failure `<FailedModel[origin=GAM[gene=None, lineage=None, model=GammaGAM(callbacks=['deviance', 'diffs'], fit_intercept=True, max_iter=2000, scale=None, terms=s(0), tol=0.0001, verbose=False)]]>`.
michalk8 commented 2 years ago

Thank you! The problem seems with passing color: TypeError: prepare() got an unexpected keyword argument 'color' Think you'd need to pass it as plot_kwargs={'cell_color': 'pterotyping_donor__anno'} cell_color='pterotyping_donor__anno'; see other options for plotting here

keithgmitchell commented 2 years ago

Ahh did not see that in the traceback, thank you!