Figure 2. The P. aeruginosa phenome landscape organized by phenotypic similarity determined by 119 phenotypes of 4030 mutants.

We systematically estimated the phenotypic distances between the genotypes, which were the basis for hierarchical clustering and multi-dimensional scaling. (A) Heat map, rows correspond to mutants and columns to different phenotypic tests. (B) Projection onto a two-dimensional grid using multi-dimensional scaling (MDS). Point colors were overlaid by seven cluster groups. (C) MDS data were converted to a contour image using two-dimensional kernel density estimation. Altitudes indicate the density of mutants in the MDS grid. (D) The contour image was depicted as a three-dimensional landscape, in which phenotypically similar mutants are located close to each other, the height indicating the density of mutants in that region of the phenotypic space.