fixed bug in calc_diff_abund_deseq2

[ethanbass]

Hi,
Great package! I found a bug in the calc_diff_abund_deseq2 that prevents the use of factors as grouping variables.

It throws an error:

Error in cleanContrast(object, contrast, expanded = isExpanded, listValues = listValues,  : 
  2 and 1 should be levels of group such that group_2_vs_M and group_1_vs_M are contained in 'resultsNames(object)'

("M" is the name of my first factor here). I figured out it's because the DESeq2::results function requires the names of the factors as arguments to contrast, but instead the function is feeding it the factors directly. It seems to work fine if you just convert the grouping variable back to a character vector before feeding the combinations to DESeq2::result or lfcShrink.

[zachary-foster]

Looks good, thanks!