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After fixing the ranks orientation in #99 , we forgot to fix the orientation of the inputs into heatmap and paired-heatmaps.

This pull request should fix this. CC @nbokulich

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In addition, realized that the rank heatmaps look best on double centered input. Now, that command does double centering by default.

Further, it looks like the legends weren't aligned properly.
image

That is now fixed
image

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A bit of digging was done to reproduce the figures in paper

  1. The previous release was still correct - the ranks need to be column centered, not row centered (this is due to the softmax transform). The soil benchmarks support this.
  2. But for the sake of visualization, it can be useful to row center the data. Below is a scenario is an illustration of what can happen.

image

Basically here, all of the columns are biased, and aren't really comparable. The above plots in the previous post are row centered.

But rather than making this a hard-coded default, I'm adding this as an option, since the paired plots have also been shown to look better when centered

image

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Merging, then we'll cut a real release.

@mortonjt mortonjt merged commit aeae43f into biocore:master Oct 18, 2019
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