Hello,
I am interested in using the newly
added options in new qiime release, so I need your help to interpret the attached emperor plot (across axis).Thanks
Eman
Hello,
I am interested in using the newly
added options in new qiime release, so I need your help to interpret the attached emperor plot (across axis).Thanks
Eman
Hello Eman,
On the ‘normal’ PCoA plot, the principal coordinates are set up like the dimensions of a cube:
 pc2

_ _ _ pc1
/
/
/ pc3
Only one problem with cubes: They only have 3 dimensions!
Because you have more than 3 principal coordinates, you want a way to see more than just 3 of them. This plot let’s you see more of them:
     
     
     
     
pc1 pc2 pc3 pc4 pc5 pc6
I hope this helps!
Colin
Thanks a lot and sorry for my delayed reply since the forum notification was sent to the promotions not the main box.
I can see different shifts between samples of 2 different treatments on each axis. So, when interpreting or reading the plot, the focus should be on the axis that captured most of the information (e.g., here, partial shift in the microbiome from axis 1).
Thanks
Eman
Correct! Principal Coordinate 1 will always capture the largest amount of information, but one of the other axis might capture an important separation between groups of samples. So PC5 might show a clear separation between treatment A and B, which you would never have seen on PC1, PC2, PC3 in the 3D graph.
vs
Colin
Thanks so much for the explanation!
Eman
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