main {Plasmidprofiler} | R Documentation |
Run all the interim functions to produce outputs. Can be run in order individually if desired.
read_blast
Import the blast file, add column names
blast_parser
Parse imported file
amr_positives
Detect AMR positive plasmids
read_srst2
Import SRST2 file
combine_results
Combine SRST2 and Blast
zetner_score
Add Sureness value
amr_presence
Add detected AMR to report
subsampler
Apply filters to report
order_report
Arrange report
save_files
Save JPG and CSV
create_plotly
Creates plot
save_files
Save HTML plot
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")
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 |
Saves output files in working directory
main(blastdata,
srst2data,
coverage.filter=NA,
sureness.filter=0.75,
length.filter=10000,
main.title="Example Results")