Beta Diversity Trees

[thermokarst]

Hi @Sara_Jeanne08.

@Sara_Jeanne08

I did not realize I needed a new mapping file - as I had the IDs in the Base_Sample Column

I would recommend reviewing the Metadata in QIIME 2 tutorial for more information on how metadata works in QIIME 2.

@Sara_Jeanne08

Curious do I need to remake my tree to match up with these IDs when I run phylogenetic-based diversity tests.

The tree tips are comprised of Feature IDs, not Sample IDs (going back to the idea of a feature table, this is the other axis). The phylogenetic metrics are designed to work with trees that are a superset of IDs - for example, you could use the full greengenes tree with your feature table. You should be fine to just use your existing tree. Thanks!

[Sara_Jeanne08 (Sara D.)]

Hi @thermokarst,

Thank you again for all your help. My analyses are going well but I had a few warnings pop up that I wanted to ask you about:
Command:
(qiime2-2017.12) bash-3.2$ qiime diversity beta-rarefaction --i-table 20180403_PhII_SILK_ONLY_VSearch_OpenRef_99per_Clustered_Table_10OTUsmin_NoSgM9_NoUnAssigned_GROUPED_MEAN.qza --i-phylogeny ../20180225_PHII_All_VSearch_OpenRef_99per_Clustered_Seqs_10OTUsmin_NoSgM9_NoUnAssigned_MidPoint_Rooted_TREE.qza --p-metric jaccard --p-clustering-method upgma --m-metadata-file 20180304_Spider_Microbiome_SILK_ONLY_Mapping_FIle_COLLAPSED.txt --p-sampling-depth 28629 --output-dir 20180404_Beta_Div_Jaccard --verbose

 /Users/Sara_Jeanne/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/sklearn/utils/validation.py:475: DataConversionWarning: Data with input dtype int64 was converted to bool by check_pairwise_arrays.
  warnings.warn(msg, DataConversionWarning)
/Users/Sara_Jeanne/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/emperor/core.py:204: FutureWarning: 
Passing list-likes to .loc or [] with any missing label will raise
KeyError in the future, you can use .reindex() as an alternative.

I still am getting the output files but I am wondering what this warning actually means... I have run this test many times on different base sample types but this is the first I am seeing this warning.

Thank you,

Sara

[thermokarst]

Hi @Sara_Jeanne08, that is a deprecation warning, intended to warn users of the pandas tool of a now-deprecated behavior of that tool. In this instance, the warning is coming from code in the emperor tool (emperor is using pandas internally). The TLDR is that this is out of your hands, and shouldn't be a cause for any concern. I will cc @yoshiki, lead developer of Emperor to see if he wants to add anything else to this. Thanks!

[yoshiki (Yoshiki Vázquez Baeza)]

@Sara_Jeanne08

Passing list-likes to .loc or with any missing label will raise

Thanks for pointing this out @thermokarst. @Sara_Jeanne08, this is not something that should cause any concern or problems in your analyses.

Further detail:

I've looked in detail at the offending line and the warning from Pandas. The version of Emperor that raised this error relied on that functionality in Pandas to subset the samples and metadata. Fortunately for us we removed that assumption in the latest release of Emperor (not yet available in the QIIME2 distribution). This shouldn't be a problem in the future.