Visualization of Plasmid Profile Results

Documentation for package ‘Plasmidprofiler’ version 0.1.6

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 after the following steps. Blast data from attached blastdata table SRST2 data from attached srst2data table
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