Gneiss gradient clustering- metadata categorical no longer an option?

Hi Gneiss folks,
I’m in the process of running the 88 soils tutorial and I’m hoping for a little clarification. With the qiime2 2018.2 release, the metadata-category option have been removed and the error message thrown indicates that users are to use metadata column instead. Below are the two commands effected:

qiime gneiss gradient-clustering
–i-table 88soils_filt100.biom.qza
–m-gradient-file 88soils_metadata.txt
–m-gradient-category ph
–o-clustering ph_tree.nwk.qza

qiime gneiss dendrogram-heatmap
–i-table 88soils_composition.biom.qza
–i-tree ph_tree.nwk.qza
–m-metadata-file 88soils_rounded_metadata.txt
–m-metadata-category “ph_rounded”
–o-visualization “ph_heatmap”
–p-ndim 10 --verbose

Appears to work for the gradient-clustering command, however during the dendrogram-heatmap step, the --m-metadata-category option is gone, but --m-metadata-column throws the error that the values in the column cannot be a numerical value. Is there a work around for this issue?


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Hi @balford, this something that has popped up when trying to differentiate between categorical and continuous data. Since rounded pH values are still numeric, we are still cutting too many corners with the new type system.

The easiest way around this is casting these values to categories. I have an example of that same metadata file here where I just add an extra _ character after each number.

Good hack @mortonjt! Even better, you can just use the #q2:types directive to declare those values as categorical!


Thanks! Raised issue here.

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Good work around. Thanks James!

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