Consistency and robustness of compartmental separation within and between gradients.

Manhattan distances among markers for each gradient were converted into a principal coordinates (PCo) space using classical multidimensional scaling (CMD) for the three independent and 729 non-redundant combinations of randomly assembled gradients. Shapes colored in magenta show the data points for the three independent gradients (G1, G2, and G3 as depicted in the figure) of each selected marker. Data points from simulated gradients are depicted as circles with coloration according to the individual compartments: green – chloroplasts, blue – cytosol, and grey – vacuole. For each compartment the 95% confidence ellipse is drawn as a dashed grey line on the basis of the mean, standard deviation, and correlation of the 729 non-redundant gradient combinations. The mitochondrial compartment (yellow circles) shows an overlapping distribution with the cytosol where the majority of data are in between the plastidic and cytosolic compartments. The principal coordinates 1 and 2 explain together in average about 96.7% of the total variance of the underlying distance matrices. For each of the three resolved compartments the distribution of average abundances including their standard deviations throughout the three independent gradients is depicted as bar plots.