ah, interesting. thanks


On Tue, Nov 26, 2013 at 2:30 PM, J W Debelius <notifications@github.com>wrote:

> In americangut/make_phyla_plots.py:
>
> > -    # Gets the sample ids from the otu table
> > -    sample_ids = list(otu_table.SampleIds)
> > -
> > -    # Determines the total number of counts in the table
> > -    table_total = otu_table.sum('sample')
> > +    num_cats = len(common_categories)
> > +
> > +    sample_ids = list(biom_table.SampleIds)
> > +    num_samples = len(sample_ids)
> > +
> > +    # Normalizes the biom table
> > +    biom_norm = biom_table.normObservationBySample()
> > +    # Prealocates numpy objects (because that makes life fun!). tax_other is
> > +    # set up as a row array because this is ultimately summed
> > +    cat_summary = zeros([num_cats, num_samples])
> > +    cat_other = zeros([1, num_samples])
>
> Vstack requires an m x n matrix, it throws an error when I pass a vector
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/qiime/American-Gut/pull/44/files#r7940439>
> .
>