Visualizing MAGIC values on PCA

[CYZou]

Hi, I have some problem on MAGIC in R. I successfully installed Rmagic and python. I followed the tutorial and everything seems to be fine. I have no problem to run magic but when I tried to do the PCA visualization with "bmmsc_MAGIC_PCA <- magic(bmmsc, genes="pca_only", t=4, init=bmmsc_MAGIC)", error showed up as

Error in py_call_impl(callable, dots$args, dots$keywords) : TypeError: '<=' not supported between instances of 'NoneType' and 'int' Detailed traceback: File "/Users/chengyuzou/Library/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages/magic/magic.py", line 405, in set_params self._check_params() File "/Users/chengyuzou/Library/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages/magic/magic.py", line 225, in _check_params utils.check_positive(knn=self.knn) File "/Users/chengyuzou/Library/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages/magic/utils.py", line 22, in check_positive if params[p] <= 0:

Any suggestions how to fix it? Thanks!

[scottgigante]

@CYZou can you please fill in the bug report template? It contains a lot of diagnostic information I need from you.

Describe the bug A clear and concise description of what the bug is.

To Reproduce Standalone code to reproduce the error

Expected behavior A clear and concise description of what you expected to happen.

Actual behavior Please include the full traceback of any errors

System information:

Output of magic.__version__:

If you are running MAGIC in R or Python, please run magic.__version__ and paste the results here.

You can do this with `python -c 'import magic; print(magic.__version__)'`

Output of pd.show_versions():

If you are running MAGIC in R or Python, please run pd.show_versions() and paste the results here.

You can do this with `python -c 'import pandas as pd; pd.show_versions()'`

Output of sessionInfo():

If you are running MAGIC in R, please run sessionInfo() and paste the results here.

You can do this with `R -e 'library(Rmagic); sessionInfo()'`

Output of reticulate::py_discover_config(required_module = "magic"):

If you are running MAGIC in R, please run `reticulate::py_discover_config(required_module = "magic")` and paste the results here.

You can do this with `R -e 'reticulate::py_discover_config(required_module = "magic")'`

Additional context Add any other context about the problem here.

[scottgigante]

@CYZou did you resolve this issue?