Longitudinal microbiome analysis


I am using "Longitudinal microbiome analysis" for my own data set. The output doesn't make any sense to me- probably, I am having trouble interpreting the output or doing something incorrectly. I have different timepoints labeled and "periods" in my metadata and I used code " qiime longitudinal volatility *
** --i-table genus-rf-table.qza *

** --p-state-column period**
** --m-metadata-file 16S_WA.tsv uu-umap.qza diversity-core-metrics-phylogenetic/faith_pd_vector.qza diversity-core-metrics-phylogenetic/evenness_vector.qza diversity-core-metrics-phylogenetic/shannon_vector.qza **
** --p-individual-id-column SeqID **
** --p-default-group-column condition **
** --o-visualization volatility-plot-1.qzv** "
to generate my volatility plot. I expect to see different trends in my variables over the period time. I have two concerns. 1. all variables show the same trends, 2. I can only view one variable at a time.

Any comments/feedback will be highly helpful. Thank you!

volatility-plot-1.qzv (830.8 KB)

metadata-16S_WA.qzv (1.2 MB)

I think the issue is here:
--p-individual-id-column SeqID **

I noticed that these are all unique. However, the individual-id is supposed to have duplicate values, with one value for each individual, and each individual having multiple IDs in this column.

Your second to last column has the values you want:


Try rerunning with that column and let us know what you find.

1 Like

Thank you @colinbrislawn

That makes sense. I changed the column --p-individual-id-column period (Because I am interested to see what genera contribute over the period of time.

It solves my problem. Thank you so much for guiding me.

accuracy_results.qzv (517.6 KB)

volatility_plot.qzv (826.3 KB)

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.