Powergraph labels

[aassie]

Hello, me again,

I have a couple of questions about the m2m_analysis workflow.

1. Would it be possible to change the taxonomy level of the stat summary steps? The class level is not really informative for what I am looking at and I was wondering if it could be changed to any lower level

2. I was looking at the powergraph output from the m2m pipeline and it seems that at some point my bacteria names got changed to their taxonomies but I can't find how to link their changed names to the original. Is there a way to keep the original name in the figure?

Example below:

[cfrioux]

Hello Adrien,

I'll try to answer to both of your questions. So far m2m_analysis is not as flexible as it could be as it was implemented mainly in order to reproduce the figures from our manuscript.

1 - By default we look at the phylum and no other taxonomic level. We might modify that in the near future. I know that @ArnaudBelcour intends to work again on m2m_analysis over the next few weeks. In the meantime should you want to look at the genus-level for instance, you could modify the code in this function, and in particular L315 which is where we retrieve the first four characters of phylum for counting. If you change rank[0] for rank[4], you will calculate your stats at the genus level.

2 - Indeed we introduced a mapping step in the code in order to prevent long names to decrease readability in the figure. The matching between the new names and the original ones is given in output_dir/taxon_phylum.tsv. If you do not want such mapping to be done, you can rerun the analysis without the --taxon taxon_id.tsv argument. See the attached figures that were generated with and without the --taxon argument.

I hope this helps, please let me know if this is unclear.

[aassie]

Thank you very much for your replies!

Sorry about 2) that I missed that file in my output directory!

[cfrioux]

No worries, we will clarify the documentation.