Taxa plot- level 7

[2508 (Atara Uzan)]

Hi
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?
thanks
Atara

[colinbrislawn (Colin J Brislawn)]

Hello Atara,

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.

is it possible that the taxa plot combine 6 different feature?

That is possible! Let’s take a look at the command to make sure.

Colin

[2508 (Atara Uzan)]

hi
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

Thank you!

[colinbrislawn (Colin J Brislawn)]

Hello Atara,

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.

Colin

[thermokarst]

Hi @2508!

using dada2 Im assuming that every feature is a taxa

@jairideout has a nice summary about this:

ANCOM results found bug?

each feature in your feature table represents a single Amplicon Sequence Variant (ASV), i.e. a biological sequence. Different ASVs can map to the same taxon (for example, the same genus) – in other words, ASVs don’t necessarily correspond to different taxa. The same idea applies to OTUs – for example, if you’ve clustered your sequences into 97% OTUs, different OTU representative sequences may map to the same genus.

So in your case, each ASV doesn’t necessarily represent a different taxon, just that each of those features are unique amplicon sequence variants.

You are correct! And this plugin does combine taxa in exactly this way.

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!

[2508 (Atara Uzan)]

Are you interested in looking at specific features?

Is it possible to create taxa plot without combining all the unspecified species?

[2508 (Atara Uzan)]

@jairideout summarize it very nicely!
Thank you vers much for the answer!

[thermokarst]

Is it possible to create taxa plot without combining all the unspecified species?

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!