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broadinstitute / wot

A software package for analyzing snapshots of developmental processes
https://broadinstitute.github.io/wot/
BSD 3-Clause "New" or "Revised" License
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wot: error: argument command: invalid choice: 'neighborhood_graph' #71

Closed mbk0asis closed 4 years ago

mbk0asis commented 5 years ago

Hi!

I was going to test run 'wot' with the example data in the homepage, but I got stuck in the beginning.

I copied the command and pasted to run the following command wot neighborhood_graph --matrix data/ExprMatrix.var.genes.h5ad --space dmap --neighbors 50 --pca_comps 100 --diff_comps 20 --out fle-input and obtained a following error wot: error: argument command: invalid choice: 'neighborhood_graph' (choose from 'convert_matrix', 'cells_by_gene_set', 'census', 'diff_exp', 'fates', 'gene_set_scores', 'optimal_transport', 'optimal_transport_validation', 'trajectory', 'trajectory_divergence', 'trajectory_trends', 'transition_table')

I saw 'neighborhood_graph' command in the homepage, but the error said like no such tool existed. What could be the problem here?

Thank you!

joshua-gould commented 5 years ago

Sorry that part of our documentation is out of date. I've removed the command from the documentation. We now recommend using Pegasus to generate embeddings.

mbk0asis commented 5 years ago

Thank you for reply!

Is threre any tutorials I can follow for Pegasus?

2019년 10월 18일 (금) 오후 8:22, Joshua Gould notifications@github.com님이 작성:

Sorry that part of our documentation is out of date. I've removed the command from the documentation. We now recommend using Pegasus https://pegasus.readthedocs.io/en/latest/ to generate embeddings.

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joshua-gould commented 5 years ago

Documentation is available at https://pegasus.readthedocs.io/en/latest/index.html

On Tue, Oct 22, 2019 at 4:01 AM Byungkuk Min notifications@github.com wrote:

Thank you for reply!

Is threre any tutorials I can follow for Pegasus?

2019년 10월 18일 (금) 오후 8:22, Joshua Gould notifications@github.com님이 작성:

Sorry that part of our documentation is out of date. I've removed the command from the documentation. We now recommend using Pegasus https://pegasus.readthedocs.io/en/latest/ to generate embeddings.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/broadinstitute/wot/issues/71?email_source=notifications&email_token=ADHQWCCIKG46VRCALZB2SATQPGL6XA5CNFSM4JCDB3EKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEBT7NAY#issuecomment-543684227 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ADHQWCGT7K5MG7UZN4EE3XLQPGL6XANCNFSM4JCDB3EA

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mbk0asis commented 5 years ago

I'm sorry to bother you, but would you explain exactly which step I should use Pegasus?

And I'm getting another error when running 'wot trajectory_trends'. Was this command also deprecated? The command and the error message are as follow;



$ wot trajectory_trends --trajectory wot_trajectory.txt --cell_days data/cell_days.txt --matrix data/ExprMatrix.h5ad --gene_filter Nanog,Obox6,Zfp42 --plot
/usr/local/lib/python3.6/dist-packages/pegasus/__init__.py:6: UserWarning: 
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.

The backend was *originally* set to 'TkAgg' by the following code:
  File "/usr/local/bin/wot", line 7, in <module>
    from wot.__main__ import main
  File "/usr/local/lib/python3.6/dist-packages/wot/__init__.py", line 4, in <module>
    import wot.graphics
  File "/usr/local/lib/python3.6/dist-packages/wot/graphics/__init__.py", line 4, in <module>
    from .plot import *
  File "/usr/local/lib/python3.6/dist-packages/wot/graphics/plot.py", line 5, in <module>
    from matplotlib import pyplot as plt
  File "/usr/lib/python3/dist-packages/matplotlib/pyplot.py", line 72, in <module>
    from matplotlib.backends import pylab_setup
  File "/usr/lib/python3/dist-packages/matplotlib/backends/__init__.py", line 14, in <module>
    line for line in traceback.format_stack()

  matplotlib.use("Agg")
Transforming to str index.
Traceback (most recent call last):
  File "/usr/local/bin/wot", line 11, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.6/dist-packages/wot/__main__.py", line 23, in main
    cmd.main(args)
  File "/usr/local/lib/python3.6/dist-packages/wot/commands/trajectory_trends.py", line 32, in main
    results = wot.tmap.trajectory_trends_from_trajectory(trajectory_ds, matrix, day_field=cell_days_field)
  File "/usr/local/lib/python3.6/dist-packages/wot/tmap/util.py", line 148, in trajectory_trends_from_trajectory
    mean_ds = anndata.AnnData(mean_list[j], pd.DataFrame(index=timepoints), expression_ds.var.copy())
  File "/usr/local/lib/python3.6/dist-packages/anndata/core/anndata.py", line 570, in __init__
    filename=filename, filemode=filemode)
  File "/usr/local/lib/python3.6/dist-packages/anndata/core/anndata.py", line 762, in _init_as_actual
    ['obs_names', 'row_names', 'smp_names'])
  File "/usr/local/lib/python3.6/dist-packages/anndata/core/anndata.py", line 177, in _gen_dataframe
    anno.index = anno.index.astype(str)
  File "/usr/lib/python3/dist-packages/pandas/core/indexes/numeric.py", line 305, in astype
    self.__class__)
TypeError: Setting <class 'pandas.core.indexes.numeric.Float64Index'> dtype to anything other than float64 or object is not supported```
joshua-gould commented 5 years ago

An example for using pegasus to compute the FLE is at the bottom of https://nbviewer.jupyter.org/github/broadinstitute/wot/blob/master/notebooks/Notebook-1-FLE-cell_sets-gene_sets.ipynb .

trajectory_trends is supported. Can you please send me the command line and data that generated the error? Thanks.

On Tue, Oct 22, 2019 at 10:49 PM Byungkuk Min notifications@github.com wrote:

I'm sorry to bother you, but would you explain exactly which step I should use Pegasus?

And I'm getting another error when running 'wot trajectory_trends'. Was this command also deprecated? The command and the error message are as follow;

$ wot trajectory_trends --trajectory wot_trajectory.txt --cell_days data/cell_days.txt --matrix data/ExprMatrix.h5ad --gene_filter Nanog,Obox6,Zfp42 --plot /usr/local/lib/python3.6/dist-packages/pegasus/init.py:6: UserWarning: This call to matplotlib.use() has no effect because the backend has already been chosen; matplotlib.use() must be called before pylab, matplotlib.pyplot, or matplotlib.backends is imported for the first time.

The backend was originally set to 'TkAgg' by the following code: File "/usr/local/bin/wot", line 7, in from wot.main import main File "/usr/local/lib/python3.6/dist-packages/wot/init.py", line 4, in import wot.graphics File "/usr/local/lib/python3.6/dist-packages/wot/graphics/init.py", line 4, in from .plot import * File "/usr/local/lib/python3.6/dist-packages/wot/graphics/plot.py", line 5, in from matplotlib import pyplot as plt File "/usr/lib/python3/dist-packages/matplotlib/pyplot.py", line 72, in from matplotlib.backends import pylab_setup File "/usr/lib/python3/dist-packages/matplotlib/backends/init.py", line 14, in line for line in traceback.format_stack()

matplotlib.use("Agg") Transforming to str index. Traceback (most recent call last): File "/usr/local/bin/wot", line 11, in sys.exit(main()) File "/usr/local/lib/python3.6/dist-packages/wot/main.py", line 23, in main cmd.main(args) File "/usr/local/lib/python3.6/dist-packages/wot/commands/trajectory_trends.py", line 32, in main results = wot.tmap.trajectory_trends_from_trajectory(trajectory_ds, matrix, day_field=cell_days_field) File "/usr/local/lib/python3.6/dist-packages/wot/tmap/util.py", line 148, in trajectory_trends_from_trajectory mean_ds = anndata.AnnData(mean_list[j], pd.DataFrame(index=timepoints), expression_ds.var.copy()) File "/usr/local/lib/python3.6/dist-packages/anndata/core/anndata.py", line 570, in init filename=filename, filemode=filemode) File "/usr/local/lib/python3.6/dist-packages/anndata/core/anndata.py", line 762, in _init_as_actual ['obs_names', 'row_names', 'smp_names']) File "/usr/local/lib/python3.6/dist-packages/anndata/core/anndata.py", line 177, in _gen_dataframe anno.index = anno.index.astype(str) File "/usr/lib/python3/dist-packages/pandas/core/indexes/numeric.py", line 305, in astype self.class) TypeError: Setting <class 'pandas.core.indexes.numeric.Float64Index'> dtype to anything other than float64 or object is not supported```

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mbk0asis commented 5 years ago

Sorry for late reply. I used the example data and command presented in the tutorial page.

Thank you!