Fig. 4.

Bacterial and viral microbiota signatures are coupled with clinical outcomes in patients with CAP. Heat map (A) of the scaled sequences levels (a normally-distributed denoised representation of the input data generated by MOFA by taking the product of the factors and the weights) for the bacteria and viruses (rows) displayed in Fig. 3B,C, samples are shown in the columns and annotated by category and the value of Factor 1 in CAP patients at admission. Kaplan-Meier plots measuring time to clinical stability (B; x-axis; defined according to Halm's criteria) and length of hospital stay (C; x-axis) for the value of Factor 1 in CAP patients at admission. The cut-point on the Factor 1 value was chosen using maximally selected rank statistics. CAP patients with a low Factor 1 have lower abundances of, among others, Enterococcus and Staphylococcus spp and higher abundances of Lactococcus phage and several commensal bacteria, compared to patients with a high Factor 1. Log-rank p-values are significant if p<0•05. Adjusted p-values (for examining multiple cut-points) are calculated using the maxstat package.