Comments (6)
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```
from wot.
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.
from wot.
from wot.
from wot.
from wot.
Sorry for late reply.
I used the example data and command presented in the tutorial page.
Thank you!
from wot.
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from wot.