Taxa barplot problem with family, order and species

I’m so sorry, probably I’m confused and I don’t know how answer to these questions because I don’t well understand that means filtered by prevalence.

I understood that is referred to samples but I don’t understand very well the meaning.

I’m sorry! This is my problem

Hi @Linda_Abenaim,

No problem! Lets take a little step back.

It does have to do with samples, we are on the right track :train:

Lets talk steps for figuring out what prevalence means!

  1. Have you check out the docs for qiime feature-table filter-features-conditionally docs? Make sure to read all the parameters and their descriptions!

  2. Within the docs for this command, this is how the prevalence parameter is explained: "The minimum portion of samples that a feature must have a relative abundance of at least abundance to be retained." Does this definition make sense to you?

  3. Here is a definition of prevalence in the microbiome analysis: https://microbiome.github.io/OMA/microbiome-exploration.html#prevalence

  4. Here are some definitions of prevalence that I found online. There are not specifically microbiome related but I think they explain prevalence well. What is Prevalence? - National Institute of Mental Health (NIMH) and Prevalence - Wikipedia

After reading the linked resources, Lets try answering the questions:
What would filtering by prevalence do?
Why do you want to filter by prevalence?
What does setting a prevalence of .34 do?

Hope that helps!

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Thank you so much for your precious help like always!

After reading, maybe prevalence is the percentage of samples that have 1% of abundance? If I selected 1% of abundance of course.
So, if I put 1% of abundance and 34% of prevalence this means that I remove the ASVs that are less than 1% of abundance and are present in 34% of samples?

So, if I reduce the percentage of prevalence (probably 5-10%) can I maintain more samples?
Did I well understand ?

If I put 1% of abundance and 10% of prevalence I remove the ASVs less than 1% only in 10% of samples?

Nailed It . :hammer:

You will retain more features. You will lose samples if a sample has no features that meet the criteria, which might have been happening with your first parameters!

You are 100% right! Just to rephrase
It will be removed if the ASVs is less then 1% abundance or in less then 10% of samples. Similarly, For a ASV to be retained it has to be equal to/greater than 1% abundance and equal to or more then 10 % of samples.

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Thank you very very very much for your help!! :pray:

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Hi everyone!
I'm here again.

I tried with this command: qiime feature-table filter-features-conditionally
--i-table feature-table.qza
--p-abundance 0.01
--p-prevalence 0.10
--o-filtered-table filtered-table.qza

and this is my visualisation with taxa-bar-plot:
taxa-bar-plots-grouped-clor-mit-conditionally.qzv (416.4 KB)

This was my objective, as @jwdebelius suggested:

I saw that some ASVs are 0.8%; is it normal?
Do you think that I'm going the right way?

I also tried to do this:

and I saw that there are no differences.
taxa-bar-plots-grouped-conditionally.qzv (421.9 KB)

Continuing the discussion from Taxa barplot problem with family, order and species:

Hi @Linda_Abenaim

I agree has a percentage below 1%
d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Myroides | 0.976%
and your provenance says that you did filter on 1% abundance

Could you send me the table you got as an output for: qiime feature-table filter-features-conditionally?

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Hi @cherman2,

this is the table
table-filter-clor-mit-conditionally.qzv (512.2 KB)

Anyway, it is not a big problem for me if I have some percentage at 0.9%, it is only to understand why.

Hi @Linda_Abenaim,
I misunderstood how filter conditionally works!

At one point I said:

I was wrong :frowning_face:

The prevelance/abundance filter just says its at least 1% in at least 10% of samples. Meaning that if its 1.0% in 10% of samples and 0% in the other 90, that gives a relative abundance of like 0.1% overall. So I believe that you used the command correctly, our understanding of how it filtered was just off!

Hope that clarifies things!

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Mmm i’m a little bit confused☹️

So if I want to remove the ASV that are less than 1% of abundance what do you suggest to do?
I want to do this only for the visualization on taxa barplot.

Or maybe it is important also for ANCOM bc.. :thinking:

But for that moment I just want to remove the ASV that are less than 1%.

Hi @Linda_Abenaim.
I don't think that QIIME 2 has a way to filter on relative abundance per sample like you want.

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Ok.
Is there not a way to group the ASVs less than 1% in "others" for the taxa barplot visualisation?

I saw it in some papers.

@Linda_Abenaim,
I am not sure that qiime has that either.

It is a little bit difficult to do grouping like this because if feature 1 in sample 1 had a 20% relative abundance, but feature 1 also had a relative abundance of 1% in sample 2. Would you want feature 1 to be collapsed into other because it has a low abundance in sample 2? I don't think so because you would be missing feature 1's large presence in sample 1. This is what I mean about you wanted to filter on relative abundance per sample.

I would suggest reading the methods of the papers you saw that visualization in and seeing if you can follow their methods! Just make sure to cite them if you do!

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