plot_OTUs: Plot OTUs
In mworkentine/mattsUtils: Personal Utility Functions For Various Analysis

Makes a box plot from a list of OTUs

plot_OTUs(physeq, otus, xaxis, fill, labeller = "Genus",
  scales = "free_y", palette = "Set1", glom = NULL, dds = NULL,
  justDf = FALSE, y_scale = c("log_counts", "counts", "relative"),
  nrow = NULL, ncol = NULL)

`physeq`	a valid phyloseq object with raw OTU counts that have not been transformed.
`otus`	a character vector of OTU ids, present in physeq. Can be "all" to plot all OTUs
`xaxis`	character, the sample column to plot on the x-axis
`fill`	character, the sample column to use for colouring the boxes
`labeller`	character, taxonomy rank to label the OTUs with. Can also be "label" which will label with genus if available and family if genus is unassigned. In this case a prefix for the taxonomic rank is addes as well
`scales`	fixed or free scales, passed to facet_wrap
`palette`	RColorBrewer palette to use
`glom`	character, the taxonomic rank to glom at
`dds`	valid DESeq2 object. If present the normalized count data will be used instead of the raw count value.
`justDf`	logical, should just the data be returned instead of plotting
`y_scale`	character, the abundance scale on the y-axis. Counts are just the raw OTU counts unless a DESeq object is provided with the dds argument, in which case the normalized counts will be used. log_counts will transform the counts by log2 using a pseudcount of +0.5. relative will use the relative abundance values instead of counts. @param nrow number of facet rows, passed to facet_wrap @param ncol same as nrow but for columns