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biocore / mmvec

Neural networks for microbe-metabolite interaction analysis
BSD 3-Clause "New" or "Revised" License
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Proportion explained is out of order: axis 1 < axis 2 < axis 3 #86

Closed wasade closed 5 years ago

wasade commented 5 years ago

When visualizing biplots, the proportion explained for axis 1 is less than the proportion explained for axis 2, which is less than the proportion explained for axis 3. An example of this can be found in the screenshot below.

Typically, users of EMPeror are accustom to interpreting axis 1 as explaining the most variation in the data. At present, this ordering reflects an inversion which may catch users off guard.

image-1

mortonjt commented 5 years ago

Yes, we will want to make sure that this is consistent with previous ordinations. Adding to the version 1 agenda

FranckLejzerowicz commented 5 years ago

I would also document another issue here that's in fact related to the ordering: --> the proportions explained in the biplot are sometime >100%,

e.g. image: Screenshot 2019-09-27 at 2 07 54 PM

and when you edit the ordinations by re-ordering

Proportion explained    3
0.0010773261702244183   0.06575598584302014 0.9331666879867555

to

Proportion explained    3
0.9331666879867555  0.06575598584302014 0.0010773261702244183

It display the proportions explained correctly

e.g. image:

Screenshot 2019-09-27 at 2 26 59 PM

However, you may want to the check the consistency of the coordinates along these axes...

Thanks!

mortonjt commented 5 years ago

Thanks @wasade @FranckLejzerowicz this should be addressed now.