biocore / biocore/DEICODE

Add emperor mchelper with CF data

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#39 0 comments 0 reactions 1 assignee Claimed by @cameronmartino View on GitHub
enhancement
Dominant language
JavaScript
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37
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18
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No merged PRs in 30d

Description

In order to expedite PRs emperor mchelper should be added with the CF dataset (below). As suggested by @mortonjt in PR #38. May need the expertise of @ElDeveloper.

[Archive.zip](https://github.com/biocore/DEICODE/files/3352528/Archive.zip)

This should follow the commands:

```shell
# microbes
deicode --in-biom filtered_otus_nt.biom --output-dir deicode_microbes --n_components 3 --max_iterations 10
qiime tools import --input-path deicode_microbes/ordination.txt --output-path ordination.qza --type "PCoAResults % Properties('biplot')"
qiime emperor biplot --i-biplot ordination.qza --m-sample-metadata-file sample-metadata.txt --output-dir emperor-microbes
# metabolites
deicode --in-biom filtered_lcms_nt.biom --output-dir deicode_metabolites --n_components 3 --max_iterations 10
qiime tools import --input-path deicode_metabolites/ordination.txt --output-path ordination.qza --type "PCoAResults % Properties('biplot')"
qiime emperor biplot --i-biplot ordination.qza --m-sample-metadata-file sample-metadata.txt --output-dir emperor-metabolites
```

Generating something like the following for each PR:

#### microbes
![emperor_microbes](https://user-images.githubusercontent.com/15164295/60548528-29851500-9cd7-11e9-9b7d-9688748a3e93.png)
#### metabolites
![emperor_metabolites](https://user-images.githubusercontent.com/15164295/60548529-2a1dab80-9cd7-11e9-89ef-5261092fbbbd.png)

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