3. Plot tabs
Kleborate-viz generates a number of interactive plots that are accessed via the plot tabs (available after data upload or selection of a built-in dataset). Only those plots for which the relevant data has been uploaded will be shown.
These following tabs are always displayed after successful data upload or selection of one of the built in datasets.
The species summary tab contains two stacked bar plots. The first shows the count of genomes by resistance score and the second shows the count by virulence score. Both plots are coloured by Kleborate species assignment.
The image below shows the Global dataset subset to include only genomes assigned to the K. pneumoniae species complex.
This tab shows a bar plot of counts for sequence types (STs). By default the bars are coloured by clone types, indicating the globally-distributed multi-drug resistant and hypervirulent STs discussed in this review article. Users can alternatively use the Annotation variable dropdown box to colour the bars by the resistance and virulence genotypes described here. The number of STs displayed in the plot can be controlled using the Number of STs slider. Hover your curser over the bar segments to view the underlying data values.
The image below shows the top 20 STs represented in the Global dataset. Bars are coloured by resistance scores.
At the top of this tab you will find a scatter plot showing mean resistance and virulence scores by ST. The size of the points represents the number of genomes assigned to that ST. Hover your curser over a point to see the ST and the mean score values. Select a point in the scatter graph or type an ST of interest into the Select ST box to view the corresponding genomes in the heatmap below, which shows the presence and absence of acquired virulence (blue) and resistance (red) determinants in columns, with individual genomes shown in rows. When there are two or more genomes the rows are clustered and the cluster dendrogram shown to the right of the heatmap. Hover your curser over the heatmap to display the genome IDs.
The image below shows the mean scores for the Global dataset, wherein ST11 is selected.
This tab explores the diversity of capsule (K) loci and lipopolysaccharide (O) loci. Bar plots show the counts of genomes for each locus, coloured by clone type (default) or user selected annotation variables described here. The heatmap shows the combinations of K loci (rows) and O loci (columns) present in the genome sample. Hover your curser over the coloured rectangles to see the K/O locus combination and the number of genomes. Users can choose to view genomes of all STs (default) or a single ST specified via the Select ST box.
These tabs will only be displayed if you are viewing one of the built-in datasets or have uploaded a metadata file containing a column called 'strain' with values matching exactly to those in the Kleborate output file.
This tab shows a bar plot of counts for metadata groups as specified by the Group variable dropdown box. By default the bars are coloured by clone types, indicating the globally-distributed multi-drug resistant and hypervirulent STs discussed in this review article. Users can alternatively use the Annotation variable dropdown box to colour the bars by the resistance and virulence genotypes described described here. The number of groups displayed in the plot can be controlled using the Number of groups slider. Hover your curser over the bar segments to view the underlying data values.
This plot will only be displayed if you are viewing one of the built-in datasets or have uploaded a metadata file with columns corresponding to information regarding isolate collection (e.g. source, country; as shown in the Group variable dropdown box). The scatter plot shows mean virulence and resistance scores by metadata group as specified in the Group variable dropdown box. The size of the points represents the number of genomes assigned to that group. Points are coloured by the metadata variable specified in the Colour variable dropdown box. Hover your curser over a point to see the data values, the number of genomes (n) and the mean scores.
The image below shows the mean scores for genomes in the Global dataset, grouped by sample type and coloured by source.
This tab will only be displayed if the metadata file contains a column called 'Year'. The histogram at the top of the tab shows the number of genomes by year. Click and drag your curser over the histogram to select years to view in the plots below. The first plot shows the mean resistance (red) and virulence (blue) scores per year. The second plot shows the mean number of acquired antimicrobial-resistance (AMR) classes and genes per year. The third and fourth plots respectively show the mean prevalence of virulence and resistance determinants per year. (See the Kleborate wiki for details about the determinants that are reported, as well as the AMR genes and classes counts.) Finally, the fifth plot shows the count of genomes by year (as bars) coloured by the annotation variable selected from the dropdown box (see here for details).
The image below shows the Global dataset subset to the year 2000 onwards. Only the histogram and the first line plot are shown.
The line plots show the cumulative prevalence of K/O loci overall (top) and by group variable (bottom). The X-axes represent the number of distinct K or O loci, sorted from the most to least common overall. Use the Group variable to specify a metadata variable to group by and hover your curser over the lines to see the underlying values.
The image below shows the cumulative K locus prevalences by geographical region for the Global dataset.
These tabs will only be displayed if you are viewing the built in EuSCAPE dataset or have uploaded an MIC file containing a column called 'strain' with values matching exactly to those in the Kleborate output file.
The X-axis is stratified by combination of beta-lactamase genes ('-' = none) and OmpK mutations (wt = wildtype; mut = one or more mutation). The data points are overlaid onto the boxplots and coloured by type of OmpK mutations as per the legend. Use the MIC variable dropdown box to specify the MIC to plot and the AMR genotype box to specify the type of genotypes to display (Bla carb = carbapenemases; Bla ESBL = extended-spectrum beta-lactamases; Bla acquired = acquired narrow spectrum beta-lactamases). Hover your curser over a data point to see the underlying values.
The image below shows meropenem MICs for genomes from the EuSCAPE dataset stratified by carbapenemase-Omp genotypes.
Users have the option to download the plots and their underlying data by clicking the buttons next to the plot title. The plot will be downloaded with the current data, annotation and/or group variable selections. The data download will include only those genomes in the current selection.