[R-sig-eco] How to calculate relative abundance along taxonomical hierarchy

[Gian Maria Niccolò Benucci]

Thank you guys!
I have found a way to do it, rank by rank ("Phylum", "Class", "Order"...)
according my dataset.
Here is the code I have used
:

fungi_phyla = tax_glom(fungi, "Phylum") ## extract the taxonomic rank e.g.
Phylum
tax_table(fungi_phyla)
fungi_phyla_ab = transform_sample_counts(fungi_phyla, function(x) x/sum(x))
## calculate relative abundances
taxa_sums(fungi_phyla_ab)/20 ## divide by the number of samples to get
general relative abundance
sample_sums(fungi_phyla_ab) ## sum

Maybe there are other ways to shorten it, but it works pretty good.
Thanks for helping,
Gian




On 25 June 2015 at 12:23, Peter Solymos <solymos at ualberta.ca> wrote:

> The tax_table accessor function will give you the taxonomic ranks in a
> table according to this website:
> https://web.stanford.edu/class/bios221/labs/phyloseq/lab_phyloseq.html
>  otu_table will give you the data matrix with OTUs as *rows*. So you need
> to transpose or adjust the code I suggested before.
>
> Peter
>
> Gian Maria Niccolò Benucci <gian.benucci at gmail.com> ezt írta (2015.
> június 25., csütörtök):
>
>> Hello,
>> thank you for the replies. My dataset is something like this:
>>
>> > datafungi
>>          BR1  BR2  BR3  BR4  BR5   F1   F2   F3   F4   F5   R1   R2   R3
>> R4   R5   W1   W2   W3   W4   W5
>> OTU_1   0.08 0.13 0.56 0.90 0.91 0.36 0.05 0.02 0.13 0.11 0.00 0.00 0.15
>> 0.06 0.00 0.12 0.00 0.00 0.03 0.05
>> OTU_35  0.01 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
>> 0.00 0.00 0.00 0.01 0.00 0.01 0.06
>> OTU_4   0.01 0.00 0.00 0.00 0.00 0.00 0.01 0.31 0.08 0.00 0.07 0.05 0.00
>> 0.00 0.00 0.00 0.00 0.07 0.41 0.00
>> OTU_3   0.00 0.00 0.00 ...
>>
>> So I do not have the taxonomic hierarchy inside the normal dataset, but
>> only the OTUs.
>>
>> Anyway, have taxonomic ranks embedded it in the phyloseq object:
>>
>> > fungi
>> phyloseq-class experiment-level object
>> otu_table()   OTU Table:         [ 150 taxa and 20 samples ]
>> sample_data() Sample Data:       [ 20 samples by 5 sample variables ]
>> tax_table()   Taxonomy Table:    [ 150 taxa by 7 taxonomic ranks ]
>>
>> That's I wondered why to do it using this kind of data. I think that many
>> other researcher that work with huge species dataset (this one is not very
>> big but I worked with thousands of OTUs) will have this problem.
>> Do you have an idea how to deal with this kind of data object?
>> Thank you,
>> Gian
>>
>>
>>
>>
>>
>> On 25 June 2015 at 11:51, Peter Solymos <solymos at ualberta.ca> wrote:
>>
>> > Gian,
>> >
>> > Once you have your samples by OTU matrix row standardized, you can use a
>> > level of your hierarchy (a vector matching the columns) and the
>> > groupSums(your-matrix, 2, your-groups) function in the mefa4 package to
>> get
>> > your relative abundances.
>> >
>> > Cheers,
>> >
>> > Peter
>> >
>> > Gian Maria Niccolò Benucci <gian.benucci at gmail.com> ezt írta (2015.
>> > június 25., csütörtök):
>> >
>> >> Hello everyone,
>> >> I am working on a fungal dataset with 151 OTUs distributed in 20
>> samples.
>> >> I
>> >> have imported it as phyloseq object and as normal species matrix as
>> well
>> >> to
>> >> work with the vegan package.
>> >> I am trying to find a way to get relative abundances at different
>> >> hierarchical level goruping the abundances of the OTUs present in my
>> >> dataset. For example, if I want to know what is the relative abundance
>> of
>> >> each Phylum (or of each Family, or each Genus) how can I do? There is a
>> >> way
>> >> to do that inside R?
>> >> Thank you very much in advance,
>> >>
>> >>
>> >> --
>> >> ​Gian​
>> >>
>> >>
>> >>
>> >> *----- Do not print this email unless you really need to. Save paper
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>> >
>> >
>> >
>> > --
>> > --
>> > Péter Sólymos
>> > 780-492-8534 | solymos at ualberta.ca | peter.solymos.org
>> > Alberta Biodiversity Monitoring Institute http://www.abmi.ca
>> > Boreal Avian Modelling Project http://www.borealbirds.ca
>> >
>> >
>>
>>
>> --
>>
>>
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>
>
> --
> --
> Péter Sólymos
> 780-492-8534 | solymos at ualberta.ca | peter.solymos.org
> Alberta Biodiversity Monitoring Institute http://www.abmi.ca
> Boreal Avian Modelling Project http://www.borealbirds.ca
>
>


-- 
Nico


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