Fig. 2
A comparison of unadjusted p-values from PLMs and LMMs for the same pairs of allelic distribution patterns of AMR genes. For the E. coli data set (panels a and b) and Salmonella data set (panels c and d), respectively, a scatter plot and box plot of paired p-values are drawn on square-root transformed axes to compare the p-values. Any p-value less than 2.2×10−16 is rounded to 2.2×10−16 owing to the smallest precise floating number in our computer. In panels a and c, black diagonal lines indicate equality between p-values from these two kinds of linear models, and grey dashed lines indicate the p-value corresponding to the Bonferroni corrected p-value of 0.05, which is used in this study as a cut-off for significant associations. Associations that were only significant in PLMs, only significant in LMMs, significant in both PLMs and LMMs, and significant in neither kind of models, are represented by blue, red, purple, and grey circles, respectively