Man pages for Plasmidprofiler
Visualization of Plasmid Profile Results

amr_positivesIdentify Antimicrobial Resistance Positive Plasmids from...
amr_presenceAdds the AMR_gene column to report
blastdataExample Table of Blast Results
blast_parserBlast Results Parser Function
combine_resultsCombines SRST2 and Blast results into a single dataframe
create_grobCreate Heatmap Graphical Object
create_plotlyCreate Plotly Object
define_coloursDefining Colours Based on a Column of Data
file_cacherFilecacher
mainMain: Run everything
minmaxMinmax
normalizeNormalize
order_reportOrder the Report
plot_heatmapCreate GGPLOT Heatmap
read_blastBlast file import function
read_srst2SRST2 file import function
reportExample Complete Report after the following steps. Blast data...
save_filesSave Files
srst2dataExample Table of SRST2 Results
subsamplerSubsetting Results
tree_makerCreate Dendrogram Based on Plasmid Content
zetner_scoreAdds the Zetner Score column to report
Plasmidprofiler documentation built on May 29, 2017, 12:09 p.m.