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 |