!wget http://qiime.org/home_static/nih-cloud-apr2012/tree_metadata.txt
!filter_distance_matrix.py -i /home/ubuntu/data/distance_matrix_complete.txt -o /home/ubuntu/data/distance_matrix_complete_v3_v4_only.txt -m tree_metadata.txt -s "starting_v_region:v3,v4,full.length"
--2012-08-07 20:05:42-- http://qiime.org/home_static/nih-cloud-apr2012/tree_metadata.txt Resolving qiime.org... 216.34.181.97 Connecting to qiime.org|216.34.181.97|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 9313 (9.1K) [text/plain] Saving to: `tree_metadata.txt.1' 100%[======================================>] 9,313 --.-K/s in 0.02s 2012-08-07 20:05:42 (389 KB/s) - `tree_metadata.txt.1' saved [9313/9313]
!principal_coordinates.py -i /home/ubuntu/data/distance_matrix_complete_v3_v4_only.txt -o /home/ubuntu/data/pc_complete_v3_v4_only.txt
!make_3d_plots.py -i /home/ubuntu/data/pc_complete_v3_v4_only.txt -o /home/ubuntu/data/pcoa_plots_complete_v3_v4_only/ -m tree_metadata.txt
And the notebook simply serves these files up in /files
, so we can visit the visualization directly
NOTE: The above link is not static: to view the plot, you must run the notebook.