2. Plots
- Filters
- Map View
- Country-level plots
- Resistance frequencies within genotypes
- Drug resistance trends
- Resistance determinants within genotypes
- Genotype distributions
TyphiNET data can be filtered by the data source, and/or by time period using the controls on the left hand side of the global overview panel.
Data source options include (a) all data, (b) just locally collected data from endemic countries, or (c) just travel-associated cases. See local/travel definitions here. Data source selection can be made by clicking on the relevant button.
Time period selections can be made by using the dropdown menus to select both the start and end year.
Filter options are applied to ALL plots in the dashboard.
Filtering options and plots can be reset to the default versions when the page loads, or by clicking on the floating reset button at the bottom right of the page.
The default global overview plot shown when the page loads shows global patterns of national frequencies of ciprofloxacin non-susceptibility (CipNS; coloured as per the inset legend).
The data presented in the global overview panel can be selected using the dropdown menu on the left hand side. Current global overview options include:
- Multidrug-resistant (MDR; resistance to classical first line drugs chloramphenicol, ampicillin, and co-trimoxazole)
- Extensively drug resistant (XDR; resistant to classical first line drugs, ciprofloxacin, and third generation cephalosporins)
- Azithromycin resistant
- Ciprofloxacin non-susceptible (CipNS)
- Ciprofloxacin resistant (CipR)
- Sensitive to all drugs (no resistance-associated genes or mutations detected)
- Dominant genotype (most common S. Typhi genotype)
- H58 Genotype (Haplotype 58/4.3.1 genotypes)
- No. samples (number of samples)
Hovering the mouse over individual countries on the map will display summary statistics relevant to each plot in a tooltip.
The plus and minus icons (or mouse scrolling wheel, if present) can be used to zoom in and out of the map. The map can be repositioned by clicking the mouse anywhere on the map and dragging it by moving the cursor. Upon repositioning the map the ‘centre map’ button will appear above the zoom in/out buttons.
Country-level plots are shown below the global overview panel, by default TyphiNET shows data from all countries.
Data from a specific country are displayed when a user either (a) clicks on a country on the map, or (b) selects a country from the dropdown menu located at the top of the country-level overview panel.
Definitions and thresholds for country-level plots can be found in section 1 'Data sources and definitions'.
Within the country-level overview panel, there are four plots, detailed below:
- Resistance frequencies within genotypes
- Drug resistance trends
- Resistance determinants within genotypes
- Genotype distributions
A plot of resistance frequencies within pathogen genotypes is displayed at the top left of the country-overview panel. By default the plot shows percentages of sequences resistant to different antimicrobials for the five most resistant genotypes. Bars are coloured by drug as per the inset legend.
The top dropdown menu can be used to alternate between showing percentages or counts of sequences resistant to the different drugs.
Up to seven different pathogen genotypes can be selected at a time for visualisation using the bottom dropdown menu for the plot. The dropdown menu is annotated with frequencies of resistance (to any drug) among each pathogen genotype.
Passing the mouse over the plot displays a tooltips that provides further data on the resistance frequencies within each pathogen genotype.
A plot of drug resistance trends over time is displayed at the top right of the country-overview panel. By default the plot shows resistance frequencies for different antimicrobials per year (as lines) where n≥10 sequences are available per year (as points). Lines and points are coloured by drug as per the inset legend. By default the plot shows lines for all drugs.
The number of drugs shown can be adjusted by using the dropdown menu above the plot.
Passing the mouse over the plot displays a tooltips that provides further data on annual resistance frequencies.
A plot of resistance determinants within different pathogen genotypes is shown at the bottom left of the country-overview panel. By default the plot shows the percentage of resistance determinants (genes and mutations; including any relevant combinations) mediating resistance to fluoroquinolones (i.e. ciprofloxacin non-susceptible) by pathogen genotype. Bars are coloured by the combination of molecular determinants present as per the inset legend. By default the 10 most resistant genotypes are shown.
Different drug classes can be selected using the top dropdown menu, which will update the plots and the relevant legend.
The bottom dropdown menu can be used to alternate between showing percentages of resistance determinants for the selected drug class and raw counts.
Passing the mouse over the plot displays tooltips that provide further data on the frequencies of different molecular drivers of resistance by pathogen genotype.
A plot of genotype distributions over time can be found at the bottom right of the country-level overview panel. By default the plot shows the number of sequences belonging to each pathogen genotype over time, with stacked bars coloured by genotype as per the inset legend.
The dropdown menu can be used to alternate between showing percentages of pathogen genotypes per year and counts.
Passing the mouse over the plot displays tooltips that provide further data on the annual frequencies of different pathogen genotypes.
