Visualization of Plasmid Profile Results

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Documentation for package ‘Plasmidprofiler’ version 0.1.4

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amr_positives Identify Antimicrobial Resistance Positive Plasmids from Blast Results
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
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