Plot taxa using qiime2

[RuneGronseth (Rune Grønseth)]

Hi,
It might be that this is the wrong forum for this question, and if so, I apologize.

I have a dataset with 800 samples from 62 participants. All participants were sampled 2 times, and 11 have been sampled three times with 6 different sample types, but some without all sample types.

I’d like to generate a bar plot that compares the relative abundances (at the genus level) for these individuals (by sample type) at two (three) different time points (ie 6 charts, rel abundance at the y-axis, at the x-axis individual samples grouped by participant (2-3 bars per participant, labelled by participant id and time point). I’ve tried various tutorials using qiime2 output converted to phyloseq objects in R, but usually they struggle with the structure of our data (not all individuals have three time points, and not all individuals have all sample types) and that I’d like to see average relative abundances (the various sample types have different biomass).

Does anyone have a good strategy for doing this? I’m not very skilled in R, so any help is appreciated.

Thanks!

Rune

[thermokarst]

Hey there @RuneGronseth, sorry to get back to you so late, we have been busy working on getting the next release of QIIME 2 out the door (soon!).

If I am understanding you correctly, you could get a rough draft of this plot by using the taxa barplot visualizer, and using the built in sample sorting to sort things by your participant, time point, etc. That might give you a good initial idea, then, if you want to make a bespoke plot, you could grab the data download out of the viz and use that in the tool of your choice.

Hope that helps!