How to interpret the paralell PCoA plot

[Eman (Eman Khalaf)]

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

[colinbrislawn (Colin J Brislawn)]

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

[Eman (Eman Khalaf)]

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

[colinbrislawn (Colin J Brislawn)]

@Eman

the focus should be on the axis that captured most of the information

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

[Eman (Eman Khalaf)]

Thanks so much for the explanation!

Eman