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dpeerlab / Palantir

Single cell trajectory detection
https://palantir.readthedocs.io
GNU General Public License v2.0
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Value error: Did not find adata.var['highly_variable'] when it is actually present #51

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

image

ManuSetty commented 3 years ago

Similar to issue #52 , this might be related to scanpy version as well. As with #52 , please use the release candidate version of scanpy pip install scanpy==1.7.0rc1

sruthi-hub commented 3 years ago

Similar to issue #52 , this might be related to scanpy version as well. As with #52 , please use the release candidate version of scanpy pip install scanpy==1.7.0rc1

Thank you so much for your help! @ManuSetty