Fig. 6

Clustering analysis of coincidence cloning samples. a Principal component analysis (PCA) plot and b multidimensional scaling (MDS) plot. The PCA plot used the overall sample distances generated from regularized log-transformation of the gene-wise count data (DESeq2). The MDS plots used the Poisson sample distances generated from the gene-wise count data (DESeq2). Green dots indicate long-term infection samples, red dots indicate short-term infection samples, and blue dots indicate culture samples for comparison