main {Plasmidprofiler}

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")