I notice today that when Im doing taxa plot in qiime2 and im looking at the species level
it combined all the s_ together to one.
I will be more specific- when I examine the feature table I had 6 differerent bifidobacterium;s__ but when I look at the taxa I saw only one bifidobacterium;s__
is it possible that the taxa plot combine 6 different feature?
Can you post the full qiime command you used to make this taxa plot? That will help us figure out exactly what the script did.
That is possible! Let’s take a look at the command to make sure.
That’s the command
qiime taxa barplot --i-table forTaxaPlot-table.qza --i-taxonomy …/ok69_allmonth_taxonomy.qza --m-metadata-file …/mapping_file_ok69_abx__UPDATE_090817.tsv --o-visualization ok69_1Month_taxa-bar-plots.qzv
Why its possible? using dada2 Im assuming that every feature is a taxa and by combining 5 feature I’m combining 5 different taxa and that can change the result dramatically
You are correct! And this plugin does combine taxa in exactly this way.
While dada2 attempts to differentiate specific taxa, the
qiime taxa barplot command only attempts to provide an overview of taxa at different taxonomic levels. This is a summary of many different features, so it’s designed to be simplified.
Are you interested in looking at specific features? Are you looking for differences between groups of samples? If you have a more specific question, another plugin may perform better than this overview barplot.
@jairideout has a nice summary about this:
So in your case, each ASV doesn’t necessarily represent a different taxon, just that each of those features are unique amplicon sequence variants.
Thanks @colinbrislawn! You are correct, the
taxa barplot collapses features at each taxonomy level.
Thanks, and let us know if you have any more questions!
Is it possible to create taxa plot without combining all the unspecified species?
@jairideout summarize it very nicely!
Thank you vers much for the answer!
Hi @2508 - we don’t currently support that kind of behavior in
q2-taxa, but I have filed an issue here for us to explore this idea more. Stay tuned!
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