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dpeerlab / Palantir

Single cell trajectory detection
https://palantir.readthedocs.io
GNU General Public License v2.0
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Error running 'sce.tl.palantir(adata)' #52

Closed sruthi-hub closed 3 years ago

sruthi-hub commented 3 years ago

I am using palantir and scanpy for trajectory inference in single-cell RNA-seq dataset. There is some issue with computing Palantir diffusion maps.

  1. It gives me an error that is did not find adata.var['highly_variable'] when it is already present.
  2. It gives an error, that 'n_components' is not a valid argument, when it is.

Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] Linux-3.10.0-1127.18.2.el7.x86_64-x86_64-with-redhat-7.8-Maipo 16 logical CPU cores, x86_64

palantir version 1.0.0

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ManuSetty commented 3 years ago

Thanks for pointing this out to us. The n_components parameter is unfortunately not exposed through the scanpy interface. Could you please try using the stand along Palantir python package.

ManuSetty commented 3 years ago

Hello again. My colleague @awnimo just pointed that this a scanpy version issue. The Palantir interface with n_components exposed is still in the pre-release stage and can be installed using pip install scanpy==1.7.0rc1