I know that this fucntionality is going to be implemented in one of the new releases of Qiime2, but in case if someone need it before the corresponding update, here is a short tutorial how to perform Adonis analysis with strata (cage effect, or restricted permutations) without any knowledge of R through terminal.
First of all, you will need to obtain a modified R script from Qiime2:
run_adonis.R (759 Bytes). It was modified to accept "strata" as additional parameter. Store it somewhere you will be able to acces.
Extract a distance matrix from the distance_matrix.qza:
qiime tools export \ --input-path Core-metrics/jaccard_distance_matrix.qza \ --output-path path/
If in the matrix not all samples from metadata are represented, create a new metadata file with only samples from the matrix to avoid adonis errors.
When all files ready, run in the terminal with qiime2 activated:
#Modify variables here adonisR=path/run_adonis.R #path to the script matrix=path/distance-matrix.tsv #path to the matrix metadata=path/metadata.tsv #path to the metadata column=Column_to_test #column to test perms=999 #number of permutations njobs=2 #number of jobs/threads strata=Column_as_strata #column as strata res=path/res.tsv #path to the output file chmod +x $adonisR $adonisR $matrix $metadata $column $perms $njobs $strata $res
The run will produce the output file with a p-value of permanova test.
To run it in a pairwise mode, one will need to filter matrix and metadata files to contain only one pair for the run for each of the pairs to be tested, then p-values should be adjusted for multiple comparissons. All steps can be implemented in python for automatisation. In R, one can run it directly as R function without this script.