wot: error: argument command: invalid choice: 'neighborhood_graph' #71
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Sorry that part of our documentation is out of date.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. |
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Thank you for reply!
Is threre any tutorials I can follow for Pegasus?
2019년 10월 18일 (금) 오후 8:22, Joshua Gould <notifications@github.com>님이 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… Sorry that part of our documentation is out of date.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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Documentation is available at
https://pegasus.readthedocs.io/en/latest/index.html
…On Tue, Oct 22, 2019 at 4:01 AM Byungkuk Min ***@***.***> wrote:
Thank you for reply!
Is threre any tutorials I can follow for Pegasus?
2019년 10월 18일 (금) 오후 8:22, Joshua Gould ***@***.***>님이 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 Sorry that part of our documentation is out of date.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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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'. |
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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 ***@***.***> 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 <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```
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Sorry for late reply. Thank you! |
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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-inputand 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!
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