You can use SCNIC to do these between data type correlations. To do this I am just allowing the user to use Spearman, Pearson or Kendall-Wright correlation and making a network and correlations file so nothing too fancy. I have not implemented this functionality in q2-SCNIC at this point and have plans to in the future but it won’t be in the next month. If you want to use it in SCNIC then you can export the biom tables from your .qza's and then use those with SCNIC_analysis.py between.
Is there anything I can do to fix it?
I still have it working in a qiime2-2018.8 env, so not a big deal at the moment but I let you know about this just in case.
Best,
Luca
Hey there @llenzi! I will let @michael.shaffer reply to this, but in the meantime, I took a look at the q2-SCNIC recipe (I am not a developer of this plugin), and it looks like the recipe indicates that it is only compatible with 2018.8 (at least as far as conda is concerned). There is probably no real reason for that, maybe @michael.shaffer can update the recipe to indicate 2018.8 as a minimum version. Anyway, until you hear back from @michael.shaffer, I would suggest just continuing with your 2018.8 env, no worries about having more than one QIIME 2 env on a machine.
@thermokarst is right. I will be pushing out a big update to q2-SCNIC that will come out hopefully in the next week or two that will include an update to the qiime 2 base version. For now I’d recommend continuing to use q2-SCNIC in your 2018.8 environment.
Hello, I am following the q2-SCNIC pipeline in QIIME2 core- 2018.8 and am on the "Calculating correlations and making your network" step.
Everytime I try to run qiime SCNIC calculate-correlations --i-table test-filtered.qza --p-method sparcc --o-correlation-table fake_correls.qza
I get an error saying:
Plugin error from SCNIC:
[Errno 2] No such file or directory: 'fastspar'
Debug info has been saved to /tmp/qiime2-q2cli-err-iy4g0idr.log
Things I have tried: reinstalling everything:
conda install -c conda-forge blas=1.1
conda update -n base -c defaults conda
conda install -c lozuponelab q2-SCNIC
pip install scnic
conda install fastspar
conda update fastspar
At some point I also tried,
conda config --add channels conda-forge
conda config --add channels defaults
Nothing worked. I then tried running Spearman correlation thinking it was just an issue with fastspar and I got:
Plugin error from SCNIC:
calculate_correlations() got an unexpected keyword argument 'p_adjustment_method'
Debug info has been saved to /tmp/qiime2-q2cli-err-xd2b8aj_.log
So I think it's an issue with my SCNIC.
Any feedback would be greatly appreciated.
I was following your instructions to add q2-SCNIC to q2-2021.2
conda install -c conda-forge blas=1.1
It causes a downgrade of blas; is this necessary, or should it be avoided?
The following packages will be DOWNGRADED:
blas 2.17-openblas → 1.1-openblas
I am trying to use q2-SCNIC to generate the correlation network using the genus level table in my microbiome data. I have generated ‘network-module.qza’ file which could be imported to cytoscape according to the tutorial. I am wondering whether is it possible to directly import a .qza format network file to cytoscape for the visualization? If it is not possible import directly, could you please suggest me a possible way to import the ‘module-network.qza’ file generated by q2-SCNIC to cytoscape? Any help is greatly appreciated!
# The directory that you’re extracting to must already exist.
mkdir extracted-network/
qiime tools extract --input-path network-module.qza --output-path extracted-network/
Then, you can find network.gml in extracted-network/{random string}/data/.