Display items for clinical metagenomics paper

1. Figure: Stx2 coverage plots per positive sample, panelled with coverage barplots and/or ratios (DONE)
2. Figure: For each texture/CFU as facets, plot E. coli / Bacteroides / Firmicutes % on a per sample basis 2a. Compare 16S. (required; 16S)
3. Figure or table: MLST profiles (required; assemblies) and any potential phylogenies for non-STECs
4. Figure: SNP MST (required; mpileup)
5. Figure: Gallery of whole-chromosome coverage plots, examples of STEC and examples of other pathogens (DONE)
6. Figure: pangenome visualisation of E. coli (required; pangenomes)
7. Table: add relative proportions of headline phyla