Function reference

All functions

ESBL_col

Data: Colourscheme for the ESBL genes / alleles detected

K_col

Data: Colourscheme for K-types

Kp1tree

Data: K. pneumoniae subsp. pneumoniae mapping tree

Kp2tree

Data: K. pneumoniae subsp. quasipneumoniae mapping tree

Kp3tree

Data: K. variicola mapping tree

O_colours

Data: Colourscheme for the O-Ag loci

O_type_colours

Data: Colourscheme for the O-Ag types as predicted

ST1415tree

Data: K. pneumoniae subsp. pneumoniae ST1415 tree

ST35tree

Data: K. pneumoniae subsp. pneumoniae ST35 tree

ST39tree

Data: K. pneumoniae subsp. pneumoniae ST39 tree

all_clean_strains

Data: A list of all post-QC strains used for the analyses

date_col

Data: Colourscheme for dates (year)

main_ST

Data: Main sequence types in the dataset

main_ST_col

Data: Colourscheme for the main ST types

sample_col

Data: Colourscheme for the sample type

species_col

Data: Colourscheme for the (sub)species

test_tree

Data: Core gene tree based on the output from panaroo

ward_col

Data: Colourscheme for the main wards