Change in a specific taxon

[ptalebic (Pasha Talebi Charmchi)]

Hi,

I am really interested in examining the changes in a specific order or phyla, for example Enterobacteriales across my sample. Is there any way I can do this? Is there any way I can create a plot like the one below:

Sorry for the size but I am interested in the plot on the left (A).

If there is no option to create this in QIIME, would you please suggest another software in detail.

Thanks again for creating this amazing forum.

[kmz]

Hi,

This is what I would do: Once I have the feature table from qiime2 (after de-noising, and any other analysis you want to do) I export the feature table as a file that can be read with any programming language. I use Python and read the file in as a dataframe. Now I can do basically everything with the dataframe including making plots like you want to.

There might be a way to do this with qiime, but I don’t know of a way.

[Nicholas_Bokulich]

@ptalebic

Is there any way I can do this? Is there any way I can create a plot like the one below:

See the tutorial for q2-longitudinal at docs.qiime2.org, the volatility action can make a plot quite like this. See that tutorial and the help documentation for more details.

Good luck!

[ptalebic (Pasha Talebi Charmchi)]

Dear Nicholas

Thank you for your quick response.

Can I use this Volatility analysis to see how a specific taxon change across my samples? I have tree groups of sample (donor, pre-FMT and post-FMT). Shouldn’t I use taxonomy.qza for this plugin? my metadata doesn’t have a column containing time. I want a plot with y axis representing abundance and x axis representing the sample.

Is it possible for you to give me an example of the code I should use?

[Nicholas_Bokulich]

@ptalebic

Can I use this Volatility analysis to see how a specific taxon change across my samples?

1. collapse your feature table by taxonomic group with qiime taxa collapse
2. convert to relative frequency with qiime feature-table relative-frequency
3. input that table to volatility

For help with these individual commands see the --help documentation

[ptalebic (Pasha Talebi Charmchi)]

Thank you so much for helping me.

I got this error when I used this command:
qiime taxa collapse
--i-table table-dada2.qza
--i-taxonomy dada2-taxonomy/taxonomy.qza
--p-level 2
--o-collapsed-table analysis/phyla-table.qza

qiime feature-table relative-frequency
--i-table analysis/phyla-table.qza
--o-relative-frequency-table analysis/rel-phyla-table.qza

qiime longitudinal volatility
--i-table analysis/rel-phyla-table.qza
--m-metadata-file sample-metadata.tsv
--p-state-column day_since_fmt
--o-visualization analysis/volatility.qzv

Error: Plugin error from longitudinal:

state_column must be numeric.

I looked into this post but I couldn't figure it out.

Here is my metadata:
sample-metadata.tsv (129.4 KB)

Any help form you would be greatly appreciated

[Nicholas_Bokulich]

@ptalebic

Error: Plugin error from longitudinal:

state_column must be numeric.

I looked into this post but I couldn’t figure it out.

As described in the post you linked to, all values in the "state" column must be numeric. Looks like day_since_fmt contains lots of non-numeric values. Choose a different column or convert those values to numbers.