<jupyter_start><jupyter_text>ANOSIM and Permanova by ibd - Unweighted UniFrac<jupyter_code>!compare_categories.py -i analysis/beta/unweighted_unifrac_dm.txt \
-m mapping-file.alpha.txt \
-c ibd -o analysis/beta/anosim-unweighted-ibd --method anosim

!compare_categories.py -i analysis/beta/unweighted_unifrac_dm.txt \
-m mapping-file.alpha.txt \
-c ibd -o analysis/beta/permanova-unweighted-ibd --method permanova<jupyter_output><empty_output><jupyter_text>ANOSIM and Permanova by ibd - Weighted UniFrac<jupyter_code>!compare_categories.py -i analysis/beta/weighted_unifrac_dm.txt \
-m mapping-file.alpha.txt \
-c ibd -o analysis/beta/anosim-weighted-ibd --method anosim

!compare_categories.py -i analysis/beta/weighted_unifrac_dm.txt \
-m mapping-file.alpha.txt \
-c ibd -o analysis/beta/permanova-weighted-ibd --method permanova<jupyter_output><empty_output><jupyter_text>ANOSIM by host_subject_id - Weighted UniFrac and Unweighted UniFrac<jupyter_code>!compare_categories.py -i analysis/beta/unweighted_unifrac_dm.txt \
-m mapping-file.alpha.txt \
-c host_subject_id -o analysis/beta/anosim-unweighted-host_subject_id --method anosim

!compare_categories.py -i analysis/beta/unweighted_unifrac_dm.txt \
-m mapping-file.alpha.txt \
-c host_subject_id -o analysis/beta/permanova-unweighted-host_subject_id --method permanova

!compare_categories.py -i analysis/beta/weighted_unifrac_dm.txt \
-m mapping-file.alpha.txt \
-c host_subject_id -o analysis/beta/anosim-weighted-host_subject_id --method anosim

!compare_categories.py -i analysis/beta/weighted_unifrac_dm.txt \
-m mapping-file.alpha.txt \
-c host_subject_id -o analysis/beta/permanova-weighted-host_subject_id --method permanova<jupyter_output><empty_output><jupyter_text>Beta Diversity PlotsAdding unique columns.<jupyter_code>!make_emperor.py -i analysis/beta/unweighted_unifrac_pc.txt \
-m mapping-file.alpha.txt \
-o analysis/beta/unweighted_unifrac_emperor_pcoa_plot/ \
--add_unique_columns

!make_emperor.py -i analysis/beta/weighted_unifrac_pc.txt \
-m mapping-file.alpha.txt \
-o analysis/beta/weighted_unifrac_emperor_pcoa_plot/ \
--add_unique_columns<jupyter_output><empty_output><jupyter_text>Vectors<jupyter_code>!make_emperor.py -i analysis/beta/unweighted_unifrac_pc.txt \
-m mapping-file.alpha.txt \
-o analysis/beta/unweighted_unifrac_emperor_pcoa_plot_vectors/ \
--add_unique_columns --add_vectors 'host_subject_id,days_since_epoch'

!make_emperor.py -i analysis/beta/weighted_unifrac_pc.txt \
-m mapping-file.alpha.txt \
-o analysis/beta/weighted_unifrac_emperor_pcoa_plot_vectors/ \
--add_unique_columns --add_vectors 'host_subject_id,days_since_epoch'<jupyter_output><empty_output>
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