Taxonomy table data structure

[mlbendall]

There are a few issues with the way we have taxonomy table currently in PathoStat. Hope this can start a discussion about how we want to handle these things.

• Should be able to get the ranks without hard coding.
  tax.name is hard-coded in ui.R. I've solved this without hard-coding in the core OTU module by getting the ranks from the PathoStat object using rank_names(). However I don't think that phyloseq enforces whether the rank names are ordered. I suggest we override rank_names() and somehow enforce the hierarchical order.
• Issues with "no rank".
  Classifications that do not fall into the usual taxonomic ranks are called "no rank" by NCBI. However, these classifications do not correspond to the same level! Sometimes this is a group ("Terrabacteria group"), sometimes this is "cellular organisms", sometimes it is a strain or other classification. The way it is handled now, all these are treated as a taxonomic rank. Also, as currently implemented, OTUs with multiple "no rank" classifications are overwritten. This should be changed If we consider the "no rank" information to be valuable.
• Issues with "others"
  Not sure if this is a problem with the sample data or the way it is loaded, but there should not be "others" when loading the full data.
• Missing data
  Many OTUs have missing. Should we propagate data from higher taxonomic levels to fill-in this missing data? For example, if OTUs are missing data from the class level, but have information at the phylum level, should we fill in the "class" field with the phylum? (This is how I've dealt with this issue in previous analyses.)

[mlbendall]

Also we need to keep in mind that we need the taxonomy to be flexible and configurable, since the taxonomy may actually represent functions or COGs (or something else) in the future.