R: Main: Run everything

main {Plasmidprofiler} | R Documentation

## Main: Run everything

### Description

Run all the interim functions to produce outputs. Can be run in order individually if desired.

1. `read_blast` Import the blast file, add column names

2. `blast_parser` Parse imported file

3. `amr_positives` Detect AMR positive plasmids

4. `read_srst2` Import SRST2 file

5. `combine_results` Combine SRST2 and Blast

6. `zetner_score` Add Sureness value

7. `amr_presence` Add detected AMR to report

8. `subsampler` Apply filters to report

9. `order_report` Arrange report

10. `save_files` Save JPG and CSV

11. `create_plotly` Creates plot

12. `save_files` Save HTML plot

### Usage

    main(blast.file, srst2.file, coverage.filter = NA, sureness.filter = NA,
      length.filter = NA, combine.inc = NA, plotly.user, plotly.api,
      post.plotly = NA, anonymize = NA, main.title = "Plasmid Profiles")

### Arguments

`blast.file` | Either system location of blast results (tsv) or dataframe
`srst2.file` | Either system location of srst2 results (tsv) or dataframe
`coverage.filter` | Filters results below percent read coverage specified (eg. 80)
`sureness.filter` | Filters results below sureness specified (eg. 0.75)
`length.filter` | Filters plasmid sequences shorter than length specified (eg. 10000)
`combine.inc` | Flag to combine incompatibility sub-groups into their main type (set to 1)
`plotly.user` | Enter your plotly info to upload to (Plotly)
`plotly.api` | Enter your plotly info to upload to (Plotly)
`post.plotly` | Flag to post to (Plotly)
`anonymize` | Flag to post to anonymize plasmids and samples (set to 1)
`main.title` | A title for the figure

### Value

Saves output files in working directory

### Examples

    main(blastdata,
    srst2data,
    coverage.filter=NA,
    sureness.filter=0.75,
    length.filter=10000,
    main.title="Example Results")

[Package Plasmidprofiler version 0.1.6 Index]