Fig. 4: Bee swarm plot of SHAP-calculation for the ten highest ranking genes for each of the E. coli antibiotic ML models. | Nature Communications

Fig. 4: Bee swarm plot of SHAP-calculation for the ten highest ranking genes for each of the E. coli antibiotic ML models.

From: Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China

Fig. 4

Genes are sorted by their mean absolute SHAP value in descending order with genes carrying most important features (SNP or accessory gene) at the top. Genes labels as ‘group_’ are unannotated genes. Each dot corresponds to one isolate in the study. The colour red indicates the presence of the feature while the colour blue indicates its absence. The bee swarm plot shows how the different feature in each isolate affects the prediction of the ML model towards resistance to the respective antibiotic. Positive SHAP values indicate a change in the expected model prediction towards resistance, while negative SHAP values indicate a change towards susceptibility. The plot is based on the ML model with all selected features included.

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