biplot

# Get collapsed data previous done whitin ANCOM preprocessing - use the filter table
qiime feature-table filter-features \
--i-table ggtable.qza \
--p-min-frequency 2434 \
--p-min-samples 10 \
--o-filtered-table table_abund.qza

# We’re also often interested in performing a differential abundance test at a specific taxonomic level. 
# To do this, we can collapse the features in our FeatureTable[Frequency] at the taxonomic level of interest (using the filtered table_abund.qza), 
# and then re-run the above steps. In this tutorial, we collapse our feature table at the species level (i.e. level 7 of the Greengenes taxonomy).
qiime taxa collapse \
  --i-table table_abund.qza \
  --i-taxonomy taxonomy.qza \
  --p-level 7 \
  --o-collapsed-table species-collapse.qza

qiime taxa collapse \
  --i-table table_abund.qza \
  --i-taxonomy taxonomy.qza \
  --p-level 2 \
  --o-collapsed-table phylo-collapse.qza

# Create a relative frequency table from collapsed taxa
qiime feature-table relative-frequency \
--i-table species-collapse.qza \
--o-relative-frequency-table species-relfreq-table.qza

qiime feature-table relative-frequency \
--i-table phylo-collapse.qza \
--o-relative-frequency-table phylo-relfreq-table.qza

# For some reason, the qiime diversity core-metrics-phylogenetic pipeline returns ans error for creating the PCOA
# for doing the biplot - create the PCOA from the distance matrix on the core-metrics-results folder
qiime diversity pcoa \
--i-distance-matrix bray_curtis_distance_matrix.qza \
--p-number-of-dimensions 3 \
--o-pcoa bray_curtis_pcoa_results.qza

# Create the biplot accordingly to the distance of choice (in this case bray-curtis distance matrix)
qiime diversity pcoa-biplot \
--i-pcoa bray_curtis_pcoa_results.qza \
--i-features species-relfreq-table.qza \
--o-biplot biplot_species_bc.qza

qiime diversity pcoa-biplot \
--i-pcoa bray_curtis_pcoa_results.qza \
--i-features phylo-relfreq-table.qza \
--o-biplot biplot_phylo_bc.qza

# Visualize the biplot on EMPEROR
qiime emperor biplot \
--i-biplot biplot_species_bc.qza \
--m-sample-metadata-file metadata.tsv \
--p-ignore-missing-samples \
--p-number-of-features 14 \
--o-visualization biplot_species_bc_14.qzv \
# --verbose

qiime emperor biplot \
--i-biplot biplot_phylo_bc.qza \
--m-sample-metadata-file metadata.tsv \
--p-ignore-missing-samples \
--p-number-of-features 9 \
--o-visualization biplot_phylo_bc_9.qzv \
# --verbose

# Export files .qza to visualze the coordenates
qiime tools export \
--input-path biplot_species_bc.qza \
--output-path exported-biplot-species

qiime tools export \
--input-path biplot_phylo_bc.qza \
--output-path exported-biplot-phylo