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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
Figure 2) PCoA plot of procrustes analysis on gut body habitat wk1vswk2
| 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