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:
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.
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.
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?
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
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.