Man pages for phac-nml/plasmidprofiler
Visualization of Plasmid Profile Results
| amr_positives | Identify Antimicrobial Resistance Positive Plasmids from... |
| amr_presence | Adds the AMR_gene column to report |
| blastdata | Example Table of Blast Results |
| blast_parser | Blast Results Parser Function |
| combine_results | Combines SRST2 and Blast results into a single dataframe |
| create_grob | Create Heatmap Graphical Object |
| create_plotly | Create Plotly Object |
| define_colours | Defining Colours Based on a Column of Data |
| file_cacher | Filecacher |
| main | Main: Run everything |
| minmax | Minmax |
| normalize | Normalize |
| order_report | Order the Report |
| plot_heatmap | Create GGPLOT Heatmap |
| read_blast | Blast file import function |
| read_srst2 | SRST2 file import function |
| report | Example Complete Report after the following steps. Blast data... |
| save_files | Save Files |
| srst2data | Example Table of SRST2 Results |
| subsampler | Subsetting Results |
| tree_maker | Create Dendrogram Based on Plasmid Content |
| zetner_score | Adds the Zetner Score column to report |
