-
Notifications
You must be signed in to change notification settings - Fork 3
Looking at Similarity in Body Habitats over time using Procrustes Analysis and ANOSIM PERMANOVA
Basically what I found after running Procrustes analysis and looking at Week 1 versus every other week is that all of these have high M^2 values. The plots that usually look the most promising are the 2nd week versus the first. Occasionally however a later week compared well against the previous week when looking at the 3d PCoA plots. An example of this is week 10 vs wk 1 in the gut habitat. The points look grouped together and the distances are not as far as in other weeks.
Comment from Greg: These are really high M^2 values, so despite the statistically significant p-values, we can't report this as a good result. It's surprising to me that the Procrustes analyses aren't looking better, but one thing that is apparent from the per-individual distance comparisons is that quite a lot of individuals have a higher median distance across weeks than the median across-individual distance, so perhaps we're noticing that same result here.
Figure 1) PCoA plot of procrustes analysis on gut body habitat wk1vswk10
Week 1 vs Week# | p-value | M^2 values |
---|---|---|
wk1vswk2 | 0.00 | .674 |
wk1vswk3 | 0.00 | .641 |
wk1vswk4 | 0.00 | .613 |
wk1vswk5 | 0.00 | .651 |
wk1vswk6 | 0.00 | .771 |
wk1vswk7 | 0.00 | .741 |
wk1vswk8 | 0.00 | .775 |
wk1vswk9 | 0.00 | .631 |
wk1vswk10 | 0.00 | .763 |
wk1vswk11 | 0.00 | .760 |
wk1vswk12 | 0.00 | .626 |
Week 1 vs Week# | p-value | M^2 values |
---|---|---|
wk1vswk2 | 0.00 | .651 |
wk1vswk3 | 0.00 | .651 |
wk1vswk4 | 0.00 | .756 |
wk1vswk5 | 0.00 | .773 |
wk1vswk6 | 0.00 | .732 |
wk1vswk7 | 0.00 | .738 |
wk1vswk8 | 0.00 | .775 |
wk1vswk9 | 0.00 | .771 |
wk1vswk10 | 0.00 | .723 |
wk1vswk11 | .937 | .940 |
wk1vswk12 | .423 | .690 |
Week 1 vs Week# | p-value | M^2 values |
---|---|---|
wk1vswk2 | 0.00 | .664 |
wk1vswk3 | 0.00 | .719 |
wk1vswk4 | 0.00 | .770 |
wk1vswk5 | 0.00 | .772 |
wk1vswk6 | 0.00 | .722 |
wk1vswk7 | 0.04 | .885 |
wk1vswk8 | 0.00 | .738 |
wk1vswk9 | 0.00 | .542 |
wk1vswk10 | 0.00 | .706 |
wk1vswk11 | 0.00 | .466 |
wk1vswk12 | .053 | .489 |
Week 1 vs Week# | p-value | M^2 values |
---|---|---|
wk1vswk2 | 0.00 | .606 |
wk1vswk3 | 0.00 | .607 |
wk1vswk4 | 0.00 | .562 |
wk1vswk5 | 0.00 | .701 |
wk1vswk6 | 0.00 | .684 |
wk1vswk7 | 0.04 | .625 |
wk1vswk8 | 0.00 | .623 |
wk1vswk9 | 0.00 | .643 |
wk1vswk10 | 0.00 | .555 |
wk1vswk11 | .005 | .628 |
wk1vswk12 | 0.00 | .210 |
Body Habitat|Unweighted Anosim | Unweighted Anosim |
:----------:|:-------------------:|:-------------------:|
Palm |R-value: .615 | P-Value: .001 |
Gut |R-value: .872 | P-Value: .001 |
Tongue |R-value: .509 | P-Value: .001 |
Forehead |R-value: .65915 | P-Value: .001 |
Body Habitat|Unweighted Permanova | Unweighted Permanova |
:----------:|:-------------------:|:--------------------:|
Palm |F-value:2.52 | P-Value:0.001 |
Gut |F-value:7.608 | P-Value:0.001 |
Tongue |F-value:4.55 | P-Value:0.001 |
Forehead |F-value:2.787 | P-Value:0.001 |
Now we are working with all 10 weeks of data, we are filtering the distance matrix on a per week basis. |
---|
#gut |
#Week2 filter_distance_matrix.py -i gut_even10000_unweighted_unifrac_dm.txt -o gut_even10000_unweighted_unifrac_dm_wk1_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:1"
principal_coordinates.py -i gut_even10000_unweighted_unifrac_dm_wk1_only.txt -o gut_even10000_unweighted_unifrac_pc_wk1_only.txt
filter_distance_matrix.py -i gut_even10000_unweighted_unifrac_dm.txt -o gut_even10000_unweighted_unifrac_dm_wk2_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:2"
principal_coordinates.py -i gut_even10000_unweighted_unifrac_dm_wk2_only.txt -o gut_even10000_unweighted_unifrac_pc_wk2_only.txt
transform_coordinate_matrices.py -i gut_even10000_unweighted_unifrac_pc_wk1_only.txt,gut_even10000_unweighted_unifrac_pc_wk2_only.txt -o procrustes_wk1vwk2 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk2/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/ #Week3 filter_distance_matrix.py -i gut_even10000_unweighted_unifrac_dm.txt -o gut_even10000_unweighted_unifrac_dm_wk3_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:3"
principal_coordinates.py -i gut_even10000_unweighted_unifrac_dm_wk3_only.txt -o gut_even10000_unweighted_unifrac_pc_wk3_only.txt
transform_coordinate_matrices.py -i gut_even10000_unweighted_unifrac_pc_wk1_only.txt,gut_even10000_unweighted_unifrac_pc_wk3_only.txt -o procrustes_wk1vwk3 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk3/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/ #Week 4 filter_distance_matrix.py -i gut_even10000_unweighted_unifrac_dm.txt -o gut_even10000_unweighted_unifrac_dm_wk4_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:4"
principal_coordinates.py -i gut_even10000_unweighted_unifrac_dm_wk4_only.txt -o gut_even10000_unweighted_unifrac_pc_wk4_only.txt transform_coordinate_matrices.py -i gut_even10000_unweighted_unifrac_pc_wk1_only.txt,gut_even10000_unweighted_unifrac_pc_wk4_only.txt -o procrustes_wk1vwk4 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk4/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week 5
filter_distance_matrix.py -i gut_even10000_unweighted_unifrac_dm.txt -o gut_even10000_unweighted_unifrac_dm_wk5_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:5"
principal_coordinates.py -i gut_even10000_unweighted_unifrac_dm_wk5_only.txt -o gut_even10000_unweighted_unifrac_pc_wk5_only.txt
transform_coordinate_matrices.py -i gut_even10000_unweighted_unifrac_pc_wk1_only.txt,gut_even10000_unweighted_unifrac_pc_wk5_only.txt -o procrustes_wk1vwk5 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk5/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/ #Week 6
filter_distance_matrix.py -i gut_even10000_unweighted_unifrac_dm.txt -o gut_even10000_unweighted_unifrac_dm_wk6_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:6"
principal_coordinates.py -i gut_even10000_unweighted_unifrac_dm_wk6_only.txt -o gut_even10000_unweighted_unifrac_pc_wk6_only.txt
transform_coordinate_matrices.py -i gut_even10000_unweighted_unifrac_pc_wk1_only.txt,gut_even10000_unweighted_unifrac_pc_wk6_only.txt -o procrustes_wk1vwk6 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk6/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/ #Week 7
filter_distance_matrix.py -i gut_even10000_unweighted_unifrac_dm.txt -o gut_even10000_unweighted_unifrac_dm_wk7_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:7"
principal_coordinates.py -i gut_even10000_unweighted_unifrac_dm_wk7_only.txt -o gut_even10000_unweighted_unifrac_pc_wk7_only.txt
transform_coordinate_matrices.py -i gut_even10000_unweighted_unifrac_pc_wk1_only.txt,gut_even10000_unweighted_unifrac_pc_wk7_only.txt -o procrustes_wk1vwk7 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk7/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week8
filter_distance_matrix.py -i gut_even10000_unweighted_unifrac_dm.txt -o gut_even10000_unweighted_unifrac_dm_wk8_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:8"
principal_coordinates.py -i gut_even10000_unweighted_unifrac_dm_wk8_only.txt -o gut_even10000_unweighted_unifrac_pc_wk8_only.txt
transform_coordinate_matrices.py -i gut_even10000_unweighted_unifrac_pc_wk1_only.txt,gut_even10000_unweighted_unifrac_pc_wk8_only.txt -o procrustes_wk1vwk8 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk8/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week9
filter_distance_matrix.py -i gut_even10000_unweighted_unifrac_dm.txt -o gut_even10000_unweighted_unifrac_dm_wk9_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:9"
principal_coordinates.py -i gut_even10000_unweighted_unifrac_dm_wk9_only.txt -o gut_even10000_unweighted_unifrac_pc_wk9_only.txt
transform_coordinate_matrices.py -i gut_even10000_unweighted_unifrac_pc_wk1_only.txt,gut_even10000_unweighted_unifrac_pc_wk9_only.txt -o procrustes_wk1vwk9 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk9/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week 10
filter_distance_matrix.py -i gut_even10000_unweighted_unifrac_dm.txt -o gut_even10000_unweighted_unifrac_dm_wk10_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:10"
principal_coordinates.py -i gut_even10000_unweighted_unifrac_dm_wk10_only.txt -o gut_even10000_unweighted_unifrac_pc_wk10_only.txt
transform_coordinate_matrices.py -i gut_even10000_unweighted_unifrac_pc_wk1_only.txt,gut_even10000_unweighted_unifrac_pc_wk10_only.txt -o procrustes_wk1vwk10 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk10/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week 11
filter_distance_matrix.py -i gut_even10000_unweighted_unifrac_dm.txt -o gut_even10000_unweighted_unifrac_dm_wk11_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:11"
principal_coordinates.py -i gut_even10000_unweighted_unifrac_dm_wk11_only.txt -o gut_even10000_unweighted_unifrac_pc_wk11_only.txt
transform_coordinate_matrices.py -i gut_even10000_unweighted_unifrac_pc_wk1_only.txt,gut_even10000_unweighted_unifrac_pc_wk11_only.txt -o procrustes_wk1vwk11 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk11/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week 12
filter_distance_matrix.py -i gut_even10000_unweighted_unifrac_dm.txt -o gut_even10000_unweighted_unifrac_dm_wk12_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:12"
principal_coordinates.py -i gut_even10000_unweighted_unifrac_dm_wk12_only.txt -o gut_even10000_unweighted_unifrac_pc_wk12_only.txt
transform_coordinate_matrices.py -i gut_even10000_unweighted_unifrac_pc_wk1_only.txt,gut_even10000_unweighted_unifrac_pc_wk12_only.txt -o procrustes_wk1vwk12 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk12/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
compare_categories.py --method anosim -i gut_even10000_unweighted_ unifrac_dm.txt -o unweighted_anosim -c "PersonalID" -m ../StudentMicrobiomeProject_map.txt
compare_categories.py --method permanova -i gut_even10000_unweighted_unifrac_dm.txt -o unweighted_permanova -c "PersonalID" -m ../StudentMicrobiomeProject_map.txt -n 1000
filter_distance_matrix.py -i palm_even10000_unweighted_unifrac_dm.txt -o palm_even10000_unweighted_unifrac_dm_wk1_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:1"
principal_coordinates.py -i palm_even10000_unweighted_unifrac_dm_wk1_only.txt -o palm_even10000_unweighted_unifrac_pc_wk1_only.txt #Week 2 filter_distance_matrix.py -i palm_even10000_unweighted_unifrac_dm.txt -o palm_even10000_unweighted_unifrac_dm_wk2_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:2"
principal_coordinates.py -i palm_even10000_unweighted_unifrac_dm_wk2_only.txt -o palm_even10000_unweighted_unifrac_pc_wk2_only.txt
transform_coordinate_matrices.py -i palm_even10000_unweighted_unifrac_pc_wk1_only.txt,palm_even10000_unweighted_unifrac_pc_wk2_only.txt -o procrustes_wk1vwk2 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk2/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week3 filter_distance_matrix.py -i palm_even10000_unweighted_unifrac_dm.txt -o palm_even10000_unweighted_unifrac_dm_wk3_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:3"
principal_coordinates.py -i palm_even10000_unweighted_unifrac_dm_wk3_only.txt -o palm_even10000_unweighted_unifrac_pc_wk3_only.txt
transform_coordinate_matrices.py -i palm_even10000_unweighted_unifrac_pc_wk1_only.txt,palm_even10000_unweighted_unifrac_pc_wk3_only.txt -o procrustes_wk1vwk3 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk3/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
filter_distance_matrix.py -i palm_even10000_unweighted_unifrac_dm.txt -o palm_even10000_unweighted_unifrac_dm_wk4_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:4"
principal_coordinates.py -i palm_even10000_unweighted_unifrac_dm_wk4_only.txt -o palm_even10000_unweighted_unifrac_pc_wk4_only.txt transform_coordinate_matrices.py -i palm_even10000_unweighted_unifrac_pc_wk1_only.txt,palm_even10000_unweighted_unifrac_pc_wk4_only.txt -o procrustes_wk1vwk4 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk4/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week 5
filter_distance_matrix.py -i palm_even10000_unweighted_unifrac_dm.txt -o palm_even10000_unweighted_unifrac_dm_wk5_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:5"
principal_coordinates.py -i palm_even10000_unweighted_unifrac_dm_wk5_only.txt -o palm_even10000_unweighted_unifrac_pc_wk5_only.txt
transform_coordinate_matrices.py -i palm_even10000_unweighted_unifrac_pc_wk1_only.txt,palm_even10000_unweighted_unifrac_pc_wk5_only.txt -o procrustes_wk1vwk5 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk5/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
filter_distance_matrix.py -i palm_even10000_unweighted_unifrac_dm.txt -o palm_even10000_unweighted_unifrac_dm_wk6_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:6"
principal_coordinates.py -i palm_even10000_unweighted_unifrac_dm_wk6_only.txt -o palm_even10000_unweighted_unifrac_pc_wk6_only.txt
transform_coordinate_matrices.py -i palm_even10000_unweighted_unifrac_pc_wk1_only.txt,palm_even10000_unweighted_unifrac_pc_wk6_only.txt -o procrustes_wk1vwk6 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk6/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week 7
filter_distance_matrix.py -i palm_even10000_unweighted_unifrac_dm.txt -o palm_even10000_unweighted_unifrac_dm_wk7_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:7"
principal_coordinates.py -i palm_even10000_unweighted_unifrac_dm_wk7_only.txt -o palm_even10000_unweighted_unifrac_pc_wk7_only.txt
transform_coordinate_matrices.py -i palm_even10000_unweighted_unifrac_pc_wk1_only.txt,palm_even10000_unweighted_unifrac_pc_wk7_only.txt -o procrustes_wk1vwk7 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk7/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week8
filter_distance_matrix.py -i palm_even10000_unweighted_unifrac_dm.txt -o palm_even10000_unweighted_unifrac_dm_wk8_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:8"
principal_coordinates.py -i palm_even10000_unweighted_unifrac_dm_wk8_only.txt -o palm_even10000_unweighted_unifrac_pc_wk8_only.txt
transform_coordinate_matrices.py -i palm_even10000_unweighted_unifrac_pc_wk1_only.txt,palm_even10000_unweighted_unifrac_pc_wk8_only.txt -o procrustes_wk1vwk8 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk8/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week 9 filter_distance_matrix.py -i palm_even10000_unweighted_unifrac_dm.txt -o palm_even10000_unweighted_unifrac_dm_wk9_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:9"
principal_coordinates.py -i palm_even10000_unweighted_unifrac_dm_wk9_only.txt -o palm_even10000_unweighted_unifrac_pc_wk9_only.txt
transform_coordinate_matrices.py -i palm_even10000_unweighted_unifrac_pc_wk1_only.txt,palm_even10000_unweighted_unifrac_pc_wk9_only.txt -o procrustes_wk1vwk9 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk9/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week10
filter_distance_matrix.py -i palm_even10000_unweighted_unifrac_dm.txt -o palm_even10000_unweighted_unifrac_dm_wk10_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:10"
principal_coordinates.py -i palm_even10000_unweighted_unifrac_dm_wk10_only.txt -o palm_even10000_unweighted_unifrac_pc_wk10_only.txt
transform_coordinate_matrices.py -i palm_even10000_unweighted_unifrac_pc_wk1_only.txt,palm_even10000_unweighted_unifrac_pc_wk10_only.txt -o procrustes_wk1vwk10 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk10/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week 11
filter_distance_matrix.py -i palm_even10000_unweighted_unifrac_dm.txt -o palm_even10000_unweighted_unifrac_dm_wk11_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:11"
principal_coordinates.py -i palm_even10000_unweighted_unifrac_dm_wk11_only.txt -o palm_even10000_unweighted_unifrac_pc_wk11_only.txt
transform_coordinate_matrices.py -i palm_even10000_unweighted_unifrac_pc_wk1_only.txt,palm_even10000_unweighted_unifrac_pc_wk11_only.txt -o procrustes_wk1vwk11 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk11/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week12
filter_distance_matrix.py -i palm_even10000_unweighted_unifrac_dm.txt -o palm_even10000_unweighted_unifrac_dm_wk12_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:12"
principal_coordinates.py -i palm_even10000_unweighted_unifrac_dm_wk12_only.txt -o palm_even10000_unweighted_unifrac_pc_wk12_only.txt
transform_coordinate_matrices.py -i palm_even10000_unweighted_unifrac_pc_wk1_only.txt,palm_even10000_unweighted_unifrac_pc_wk12_only.txt -o procrustes_wk1vwk12 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk12/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#unweighted anosim compare_categories.py --method anosim -i palm_even10000_unweighted_unifrac_dm.txt -o unweighted_anosim -c "PersonalID" -m ../StudentMicrobiomeProject_map.txt #unweighted permanova compare_categories.py --method permanova -i palm_even10000_unweighted_unifrac_dm.txt -o unweighted_permanova -c "PersonalID" -m ../StudentMicrobiomeProject_map.txt -n 1000
filter_distance_matrix.py -i forehead_even10000_unweighted_unifrac_dm.txt -o forehead_even10000_unweighted_unifrac_dm_wk1_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:1"
principal_coordinates.py -i forehead_even10000_unweighted_unifrac_dm_wk1_only.txt -o forehead_even10000_unweighted_unifrac_pc_wk1_only.txt #Week2 filter_distance_matrix.py -i forehead_even10000_unweighted_unifrac_dm.txt -o forehead_even10000_unweighted_unifrac_dm_wk2_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:2"
principal_coordinates.py -i forehead_even10000_unweighted_unifrac_dm_wk2_only.txt -o forehead_even10000_unweighted_unifrac_pc_wk2_only.txt transform_coordinate_matrices.py -i forehead_even10000_unweighted_unifrac_pc_wk1_only.txt,forehead_even10000_unweighted_unifrac_pc_wk2_only.txt -o procrustes_wk1vwk2 -r 1000 -s ../procrustes_map.txt
filter_distance_matrix.py -i forehead_even10000_unweighted_unifrac_dm.txt -o forehead_even10000_unweighted_unifrac_dm_wk3_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:3"
cd procrustes_wk1vwk2/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/ #Week3 principal_coordinates.py -i forehead_even10000_unweighted_unifrac_dm_wk3_only.txt -o forehead_even10000_unweighted_unifrac_pc_wk3_only.txt
transform_coordinate_matrices.py -i forehead_even10000_unweighted_unifrac_pc_wk1_only.txt,forehead_even10000_unweighted_unifrac_pc_wk3_only.txt -o procrustes_wk1vwk3 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk3/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week4
filter_distance_matrix.py -i forehead_even10000_unweighted_unifrac_dm.txt -o forehead_even10000_unweighted_unifrac_dm_wk4_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:4"
principal_coordinates.py -i forehead_even10000_unweighted_unifrac_dm_wk4_only.txt -o forehead_even10000_unweighted_unifrac_pc_wk4_only.txt transform_coordinate_matrices.py -i forehead_even10000_unweighted_unifrac_pc_wk1_only.txt,forehead_even10000_unweighted_unifrac_pc_wk4_only.txt -o procrustes_wk1vwk4 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk4/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week5
filter_distance_matrix.py -i forehead_even10000_unweighted_unifrac_dm.txt -o forehead_even10000_unweighted_unifrac_dm_wk5_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:5"
principal_coordinates.py -i forehead_even10000_unweighted_unifrac_dm_wk5_only.txt -o forehead_even10000_unweighted_unifrac_pc_wk5_only.txt
transform_coordinate_matrices.py -i forehead_even10000_unweighted_unifrac_pc_wk1_only.txt,forehead_even10000_unweighted_unifrac_pc_wk5_only.txt -o procrustes_wk1vwk5 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk5/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week6
filter_distance_matrix.py -i forehead_even10000_unweighted_unifrac_dm.txt -o forehead_even10000_unweighted_unifrac_dm_wk6_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:6"
principal_coordinates.py -i forehead_even10000_unweighted_unifrac_dm_wk6_only.txt -o forehead_even10000_unweighted_unifrac_pc_wk6_only.txt
transform_coordinate_matrices.py -i forehead_even10000_unweighted_unifrac_pc_wk1_only.txt,forehead_even10000_unweighted_unifrac_pc_wk6_only.txt -o procrustes_wk1vwk6 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk6/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week 7
filter_distance_matrix.py -i forehead_even10000_unweighted_unifrac_dm.txt -o forehead_even10000_unweighted_unifrac_dm_wk7_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:7"
principal_coordinates.py -i forehead_even10000_unweighted_unifrac_dm_wk7_only.txt -o forehead_even10000_unweighted_unifrac_pc_wk7_only.txt
transform_coordinate_matrices.py -i forehead_even10000_unweighted_unifrac_pc_wk1_only.txt,forehead_even10000_unweighted_unifrac_pc_wk7_only.txt -o procrustes_wk1vwk7 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk7/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week8
filter_distance_matrix.py -i forehead_even10000_unweighted_unifrac_dm.txt -o forehead_even10000_unweighted_unifrac_dm_wk8_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:8"
principal_coordinates.py -i forehead_even10000_unweighted_unifrac_dm_wk8_only.txt -o forehead_even10000_unweighted_unifrac_pc_wk8_only.txt
transform_coordinate_matrices.py -i forehead_even10000_unweighted_unifrac_pc_wk1_only.txt,forehead_even10000_unweighted_unifrac_pc_wk8_only.txt -o procrustes_wk1vwk8 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk8/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week9
filter_distance_matrix.py -i forehead_even10000_unweighted_unifrac_dm.txt -o forehead_even10000_unweighted_unifrac_dm_wk9_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:9"
principal_coordinates.py -i forehead_even10000_unweighted_unifrac_dm_wk9_only.txt -o forehead_even10000_unweighted_unifrac_pc_wk9_only.txt
transform_coordinate_matrices.py -i forehead_even10000_unweighted_unifrac_pc_wk1_only.txt,forehead_even10000_unweighted_unifrac_pc_wk9_only.txt -o procrustes_wk1vwk9 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk9/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week10
filter_distance_matrix.py -i forehead_even10000_unweighted_unifrac_dm.txt -o forehead_even10000_unweighted_unifrac_dm_wk10_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:10"
principal_coordinates.py -i forehead_even10000_unweighted_unifrac_dm_wk10_only.txt -o forehead_even10000_unweighted_unifrac_pc_wk10_only.txt
transform_coordinate_matrices.py -i forehead_even10000_unweighted_unifrac_pc_wk1_only.txt,forehead_even10000_unweighted_unifrac_pc_wk10_only.txt -o procrustes_wk1vwk10 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk10/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week11
filter_distance_matrix.py -i forehead_even10000_unweighted_unifrac_dm.txt -o forehead_even10000_unweighted_unifrac_dm_wk11_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:11"
principal_coordinates.py -i forehead_even10000_unweighted_unifrac_dm_wk11_only.txt -o forehead_even10000_unweighted_unifrac_pc_wk11_only.txt
transform_coordinate_matrices.py -i forehead_even10000_unweighted_unifrac_pc_wk1_only.txt,forehead_even10000_unweighted_unifrac_pc_wk11_only.txt -o procrustes_wk1vwk11 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk11/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#anosim compare_categories.py --method anosim -i forehead_even10000_unweighted_unifrac_dm.txt -o unweighted_anosim -c "PersonalID" -m ../StudentMicrobiomeProject_map.txt #permanova compare_categories.py --method permanova -i forehead_even10000_unweighted_unifrac_dm.txt -o unweighted_permanova -c "PersonalID" -m ../StudentMicrobiomeProject_map.txt -n 1000
#Week12 filter_distance_matrix.py -i forehead_even10000_unweighted_unifrac_dm.txt -o forehead_even10000_unweighted_unifrac_dm_wk12_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:12"
principal_coordinates.py -i forehead_even10000_unweighted_unifrac_dm_wk12_only.txt -o forehead_even10000_unweighted_unifrac_pc_wk12_only.txt
transform_coordinate_matrices.py -i forehead_even10000_unweighted_unifrac_pc_wk1_only.txt,forehead_even10000_unweighted_unifrac_pc_wk12_only.txt -o procrustes_wk1vwk12 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk12/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
filter_distance_matrix.py -i tongue_even10000_unweighted_unifrac_dm.txt -o tongue_even10000_unweighted_unifrac_dm_wk1_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:1"
principal_coordinates.py -i tongue_even10000_unweighted_unifrac_dm_wk1_only.txt -o tongue_even10000_unweighted_unifrac_pc_wk1_only.txt #Week2 filter_distance_matrix.py -i tongue_even10000_unweighted_unifrac_dm.txt -o tongue_even10000_unweighted_unifrac_dm_wk2_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:2"
principal_coordinates.py -i tongue_even10000_unweighted_unifrac_dm_wk2_only.txt -o tongue_even10000_unweighted_unifrac_pc_wk2_only.txt
transform_coordinate_matrices.py -i tongue_even10000_unweighted_unifrac_pc_wk1_only.txt,tongue_even10000_unweighted_unifrac_pc_wk2_only.txt -o procrustes_wk1vwk2 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk2/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/ #Week3 filter_distance_matrix.py -i tongue_even10000_unweighted_unifrac_dm.txt -o tongue_even10000_unweighted_unifrac_dm_wk3_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:3"
principal_coordinates.py -i tongue_even10000_unweighted_unifrac_dm_wk3_only.txt -o tongue_even10000_unweighted_unifrac_pc_wk3_only.txt
transform_coordinate_matrices.py -i tongue_even10000_unweighted_unifrac_pc_wk1_only.txt,tongue_even10000_unweighted_unifrac_pc_wk3_only.txt -o procrustes_wk1vwk3 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk3/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week4
filter_distance_matrix.py -i tongue_even10000_unweighted_unifrac_dm.txt -o tongue_even10000_unweighted_unifrac_dm_wk4_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:4"
principal_coordinates.py -i tongue_even10000_unweighted_unifrac_dm_wk4_only.txt -o tongue_even10000_unweighted_unifrac_pc_wk4_only.txt transform_coordinate_matrices.py -i tongue_even10000_unweighted_unifrac_pc_wk1_only.txt,tongue_even10000_unweighted_unifrac_pc_wk4_only.txt -o procrustes_wk1vwk4 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk4/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week5
filter_distance_matrix.py -i tongue_even10000_unweighted_unifrac_dm.txt -o tongue_even10000_unweighted_unifrac_dm_wk5_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:5"
principal_coordinates.py -i tongue_even10000_unweighted_unifrac_dm_wk5_only.txt -o tongue_even10000_unweighted_unifrac_pc_wk5_only.txt
transform_coordinate_matrices.py -i tongue_even10000_unweighted_unifrac_pc_wk1_only.txt,tongue_even10000_unweighted_unifrac_pc_wk5_only.txt -o procrustes_wk1vwk5 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk5/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week 6
filter_distance_matrix.py -i tongue_even10000_unweighted_unifrac_dm.txt -o tongue_even10000_unweighted_unifrac_dm_wk6_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:6"
principal_coordinates.py -i tongue_even10000_unweighted_unifrac_dm_wk6_only.txt -o tongue_even10000_unweighted_unifrac_pc_wk6_only.txt
transform_coordinate_matrices.py -i tongue_even10000_unweighted_unifrac_pc_wk1_only.txt,tongue_even10000_unweighted_unifrac_pc_wk6_only.txt -o procrustes_wk1vwk6 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk6/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week 7
filter_distance_matrix.py -i tongue_even10000_unweighted_unifrac_dm.txt -o tongue_even10000_unweighted_unifrac_dm_wk7_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:7"
principal_coordinates.py -i tongue_even10000_unweighted_unifrac_dm_wk7_only.txt -o tongue_even10000_unweighted_unifrac_pc_wk7_only.txt
transform_coordinate_matrices.py -i tongue_even10000_unweighted_unifrac_pc_wk1_only.txt,tongue_even10000_unweighted_unifrac_pc_wk7_only.txt -o procrustes_wk1vwk7 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk7/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week8
filter_distance_matrix.py -i tongue_even10000_unweighted_unifrac_dm.txt -o tongue_even10000_unweighted_unifrac_dm_wk8_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:8"
principal_coordinates.py -i tongue_even10000_unweighted_unifrac_dm_wk8_only.txt -o tongue_even10000_unweighted_unifrac_pc_wk8_only.txt
transform_coordinate_matrices.py -i tongue_even10000_unweighted_unifrac_pc_wk1_only.txt,tongue_even10000_unweighted_unifrac_pc_wk8_only.txt -o procrustes_wk1vwk8 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk8/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week9
filter_distance_matrix.py -i tongue_even10000_unweighted_unifrac_dm.txt -o tongue_even10000_unweighted_unifrac_dm_wk9_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:9"
principal_coordinates.py -i tongue_even10000_unweighted_unifrac_dm_wk9_only.txt -o tongue_even10000_unweighted_unifrac_pc_wk9_only.txt
transform_coordinate_matrices.py -i tongue_even10000_unweighted_unifrac_pc_wk1_only.txt,tongue_even10000_unweighted_unifrac_pc_wk9_only.txt -o procrustes_wk1vwk9 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk9/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week 10
filter_distance_matrix.py -i tongue_even10000_unweighted_unifrac_dm.txt -o tongue_even10000_unweighted_unifrac_dm_wk10_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:10"
principal_coordinates.py -i tongue_even10000_unweighted_unifrac_dm_wk10_only.txt -o tongue_even10000_unweighted_unifrac_pc_wk10_only.txt
transform_coordinate_matrices.py -i tongue_even10000_unweighted_unifrac_pc_wk1_only.txt,tongue_even10000_unweighted_unifrac_pc_wk10_only.txt -o procrustes_wk1vwk10 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk10/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week11
filter_distance_matrix.py -i tongue_even10000_unweighted_unifrac_dm.txt -o tongue_even10000_unweighted_unifrac_dm_wk11_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:11"
principal_coordinates.py -i tongue_even10000_unweighted_unifrac_dm_wk11_only.txt -o tongue_even10000_unweighted_unifrac_pc_wk11_only.txt
transform_coordinate_matrices.py -i tongue_even10000_unweighted_unifrac_pc_wk1_only.txt,tongue_even10000_unweighted_unifrac_pc_wk11_only.txt -o procrustes_wk1vwk11 -r 1000 -s ../procrustes_map.txt cd procrustes_wk1vwk11/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#Week 12
filter_distance_matrix.py -i tongue_even10000_unweighted_unifrac_dm.txt -o tongue_even10000_unweighted_unifrac_dm_wk12_only.txt -m ../StudentMicrobiomeProject_map.txt -s "WeeksSinceStart:12"
principal_coordinates.py -i tongue_even10000_unweighted_unifrac_dm_wk12_only.txt -o tongue_even10000_unweighted_unifrac_pc_wk12_only.txt
transform_coordinate_matrices.py -i tongue_even10000_unweighted_unifrac_pc_wk1_only.txt,tongue_even10000_unweighted_unifrac_pc_wk12_only.txt -o procrustes_wk1vwk12 -r 1000 -s ../procrustes_map.txt
cd procrustes_wk1vwk12/
compare_3d_plots.py -i pc1_transformed.txt,pc2_transformed.txt -m ../../procrustes_plotting_map.txt -o plots/
#anosim compare_categories.py --method anosim -i tongue_even10000_unweighted_unifrac_dm.txt -o unweighted_anosim -c "PersonalID" -m ../StudentMicrobiomeProject_map.txt
#permanova compare_categories.py --method permanova -i tongue_even10000_unweighted_unifrac_dm.txt -o unweighted_permanova -c "PersonalID" -m ../StudentMicrobiomeProject_map.txt -n 1000