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franciscozorrilla / metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
https://franciscozorrilla.github.io/metaGEM/
MIT License
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Any way to make the compositionVis.R or abundanceVis.R scripts to work? #63

Closed shreyanshumale closed 3 years ago

shreyanshumale commented 3 years ago

Hello Francisco! I was trying to produce a plot similar to the one under 6. Relative abundances with bwa and samtools in the unseenbio tutorial but the compositionVis.R script does not exist. I did find an abundanceVis.R script but it needs two input files that I am unaware of: classification.stats and abundance.stats

It would be great if I could do something to make either of these work!

Thanks, Shreyansh

franciscozorrilla commented 3 years ago

Hi Shreyansh,

Thank you for pointing this out, indeed I had not updated the visualization scripts in a long time. I have now updated the config.yaml file, metaGEM.sh parser, and compositionVis.R scripts. After pulling the new code you should be able to generate the plot from the unseen_bio tutorial, please let me know if you run into any issues!

Best wishes, Francisco

franciscozorrilla commented 3 years ago

Closing this issue due to inactivity, please reopen if problems arise.