Import table of taxonomic composition with Phyloseq

[Nasute (Julissa)]

Hello everyone!

I Wish import my data shown in taxa-bar-plots.qzv to pyloseq to obtain the following: table of taxonomic composition in some downloadable format for presentation through Phyloseq

I have tried to import them using the scripts described in the Phyloseq page but I can not identify those requirements that are equivalent to the artifacts qiime2

for example:
otu_table as
sample_data as
tax_table as
phy_tree etc.,

Apparently I could import a table otu (table.qza) to the biom format, but I can not find the other elements that serve me as input to be able to graph my data obtained in qiime2 in phyloseq through RStudio

I enclose an example of the tables that I would like to present in my work but that qiime2 that qiime2 does not give the option to download as JPG

If someone has done something similar with good results and could help me, I would be very grateful

[thermokarst]

Hi @Nasute, have you had a chance to check out this community tutorial?

Get fully annotated `.biom` tables from Qiime 2 to Qiime 1 (and e.g. Phyloseq)

Dear all, I thought I share my bash script solution to get fully annotated .biom tables from Qiime 2 to Qiime 1 (and e.g. Phyloseq - including tree, sequences and metadata). You will still need to adjust this script, but it might save you some time. YOU MUST EDIT THIS SCRIPT PRIOR TO USE - AND PLEASE DO NOT RUN WITHOUT UNDERSTANDING WHAT IT DOES Kind regards, Paul #!/bin/bash ======================================================== # Converting Qiime 2 qza artifacts to Qiime 1 biom files. …

We don't develop Phyloseq, so we aren't in the best position for providing advice on how to get your data loaded there, but, if you have some concrete questions feel free to send the our way, we will see what we can do!

[Nasute (Julissa)]

Hi

@thermokarst

Effectively only try to enter my data type “artifacts qiime” to phyloseq and use several tutorials in this forum to convert them to the format “.biom” the problem is that since I started even in qiime had problems, may have to enter a pipeline from github phyloseq to know; What is the specific input format? and How to import my data to R phyloseq?

Thanks for the support!

[thermokarst]

Hi @Nasute!

@Nasute

What is the specific input format?

Have you tried the steps indicated on this post? Specifically, the second section, titled "Creating a BIOM table with taxonomy annotations"? I think you should be able to use that file as input to phyloseq (but I am not 100% sure - we aren't developers on the phyloseq project), but maybe you can give that a try? Let us know how it goes!

[Nasute (Julissa)]

Hi! @thermokarst

It is correct, I have the final file with the taxonomic annotations and in .biom format, it must be an error with the way in which I am trying to put the data.

I will keep trying, thank you very much and greetings!

[jbisanz (Jordan Bisanz)]

Hi Julissa,

Check out this tutorial I just made and let me know if the package works for you and your data:

Tutorial: Integrating QIIME2 and R for data visualization and analysis using qiime2R

Tutorial: Integrating QIIME2 and R for data visualization and analysis using qiime2R (March 2020 Update v0.99.20) Background The qiime artifact is a method for storing the input and outputs for QIIME2 along with associated metadata and provenance information about how the object was formed. This method of storing objects has a number of obvious advantages; however, on the surface it does not lend itself to easy import to R for the R-minded data scientist. In reality, the .qza file is a compres…

Jordan

[Nasute (Julissa)]

Hi @jbisanz

Thank you very much I will receive it with pleasure! regards