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Center biplot #27

Merged
merged 17 commits into from
Mar 8, 2019
Merged

Center biplot #27

merged 17 commits into from
Mar 8, 2019

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cameronmartino
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resolves issue #26

  • version 0.1.5 -> 0.1.6
  • centered features/sample ordination in both q2plugin and command line script.
  • fixed images in the tutorial to reflect the changes


# Sample Loadings
sample_loading = pd.DataFrame(opt.sample_weights, index=table.index)
sample_loading = sample_loading.rename(columns=rename_cols)
sample_loading -= sample_loading.mean(axis=0)
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This doesn't have to be resolved now, but for the lucky future developer - it looks like there is some redundancy here compared to _method.py. May want to redefine some functions to avoid copy-pasta fixes like this.

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definitely. need to merge between them.

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Another note for a future developer, there will eventually need to have unittests to test the contents of feature loadings and sample loadings -- this will become more important for regression testing to catch future bugs.

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These notes/suggestion will be lost - what about creating specific issues in the repo and adding a full description of what needs to be done + pointing here?

@mortonjt
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mortonjt commented Mar 8, 2019

@cameronmartino - don't forget to include a snapshot of the emperor plot before we merge, so that we can take a note that this issue has been resolved.

@cameronmartino
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cameronmartino commented Mar 8, 2019

@mortonjt good point.
Before:

After:

@mortonjt
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mortonjt commented Mar 8, 2019

Hmm - can't seem to see the after image ...

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mortonjt commented Mar 8, 2019

Ok - looks good. @cameronmartino don't forget to update the changelog and then I can merge this in.

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3 participants