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blekhmanlab / biomehorizon

Plot microbiome time series in parallel
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Plotting Genera instead of OTUs #12

Open michoug opened 2 years ago

michoug commented 2 years ago

Hi, I was wondering if there was an "easy" way to plot genera (probably obtained by summing the OTUs that are in this genus) instead of OTUs? Best Greg

isaacfink21 commented 2 years ago

Hi Greg, Apologies for the late response - yes, you definitely can plot genera, or any taxon, instead of OTUs. In fact, this is already done in the provided otusample_diet. If you wanted to convert an existing OTU table, you could simply sum OTU rows together grouping by taxon. If you have a taxonomydata table, you could map each taxon to its genus to form groups.

Hope this helps, let me know if you have any other questions :)