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Graphia: A platform for the graph-based visualisation and analysis of high dimensional data

Fig 5

Visualisation of the pangenome of Staphylococcus aureus.

(A) The full pangenome of 778 isolates. Nodes represent individual orthologous genes as identified by PIRATE. Node size is determined by the number of genomes in which a gene has been identified. Edges denote where two genes are syntenic, and their thickness is determined by the number of times this syntenic connection is observed across isolates. Syntenic stretches of core genes have been collapsed for clarity using the “Contract Edges” transform, and low confidence nodes and edges (n < 3) have been removed. Coloured by Weighted Louvain Clustering (granularity = 1.0). (B) Highly variable region (boxed area in A) with a high density of “phage-like” genes. Nodes and edges are sized and coloured by frequency. (C) Genes highlighted are all found in single S. aureus isolate, RF122. (D) the agrABCD locus coloured by gene-association clustering. Frequently, an alternative allele is not identified as being the same gene, but their position is strongly indicative of shared function. (E) the same locus coloured by gene identity.

Fig 5

doi: https://doi.org/10.1371/journal.pcbi.1010310.g005