I have used QIIME to analyze my data and I want to represent it for my research conference. The data needs to be presented on scientific posters (48" x 36" inch). But I can’t fit the taxa-bar-plots (it’s too long) which shows all the species present in my samples at Taxa level 7. Similarly, the phylogenetic tree is labeled by feature IDs (which are hashcodes) which will make no sense during the scientific presentation. Therefore, how can I format the QIIME data to be presented in my posters?
The out of the box figure from taxa bar plots in qiime2 is perhaps not your best options for a poster. You can have more control over your illustrations if you were to download the data and manipulate it in your own preferred program (Excel, R, Graphpad etc.), you can use the CSV button at the top of your barplot.qzv to download the raw data. Ex. this way you can trim the species names anyway you want for a cleaner legend. Or if you think the figures are fine and you just want to manipulate the legend or axis labels, you can can also download the figures and legends as a SVG and manually edit them using your preferred software (photoshop, illustrator, gimp, etc.), again this can be downloaded from the top of the barplot.qzv file.
I’m not sure if I understand which tree you are referring to, is this a visualization created outside of Q2? Either way, the feature IDs you are referring to are the exact sequence variants created by DADA2 [or Deblur]. At this part of the process taxonomy has not been assigned to them so any visualization using these will retain the originally assigned IDs.This is of course by design. You could assign taxonomy and create a feature table that resembles the former OTU tables using the taxa collapse plugin but I’m guessing for what you are trying to do, simply downloading the data (as above) and changing the bits you need would be easier?
Does that help?
p.s Just as a heads up, assignments at Taxa level 7 (species) tends to not be super accurate. Because of that, most tend to use level 6 (genus) or lower as these have higher confidence associated with their taxa assignments. So unless you have a specific reason to keep it at level 7, it might be more accurate to use level 6.
Thank you for your detailed replies!
I just used the taxa collapse and it summarizes beautifully! Thank you for being so proactive!
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