lingfeiwang
commented
6 months ago Duplicate issue https://github.com/pinellolab/STREAM/issues/144
Closed HarrisHan2k closed 6 months ago
lingfeiwang
commented
6 months ago Duplicate issue https://github.com/pinellolab/STREAM/issues/144
HI Lingfei,
I encountered this error when running the STREAM trajectory inference following the main1 textbook in the full-skin tutorial.
I prepared the data and reconstructed the adata with cell type and co-embedded UMAP coordinates. However, when I run the stream trajectory inference code in the full-skin main1 tutorial, I encountered this error:
RRuntimeError Traceback (most recent call last) /tmp/ipykernel_817251/378101491.py in 11 with TemporaryDirectory() as td: 12 st.set_workdir(adata,td) ---> 13 st.elastic_principal_graph(adata,ka1) 14 st.extend_elastic_principal_graph(adata,ka2) 15
/media/dell/Elements/soft/conda/miniconda3/envs/env_stream/lib/python3.7/site-packages/stream/core.py in elastic_principal_graph(adata, epg_n_nodes, incr_n_nodes, epg_lambda, epg_mu, epg_trimmingradius, epg_finalenergy, epg_alpha, epg_beta, epg_n_processes, use_vis, save_fig, fig_name, fig_path, fig_size, kwargs) 2026 nReps=1, 2027 ProbPoint=1.0, -> 2028 kwargs) 2029 R('dev.off()') 2030
/media/dell/Elements/soft/conda/miniconda3/envs/env_stream/lib/python3.7/site-packages/rpy2/robjects/functions.py in call(self, *args, *kwargs) 176 v = kwargs.pop(k) 177 kwargs[r_k] = v --> 178 return super(SignatureTranslatedFunction, self).call(args, **kwargs) 179 180 pattern_link = re.compile(r'\link{(.+?)}')
/media/dell/Elements/soft/conda/miniconda3/envs/env_stream/lib/python3.7/site-packages/rpy2/robjects/functions.py in call(self, *args, *kwargs) 104 for k, v in kwargs.items(): 105 new_kwargs[k] = conversion.py2ri(v) --> 106 res = super(Function, self).call(new_args, **new_kwargs) 107 res = conversion.ri2ro(res) 108 return res
RRuntimeError: Error: object ‘palette.colors’ is not exported by 'namespace:grDevices'
It seemed like the R used for stream did not have palette.colors function in their build-in grDevices package, could I see the environment you use for STREAM trajectory inference?