feature space dimensions for the kernel algorithm (b). We set k=square root of the number of pathways, m=square root of k, l=1 (default), w=1 (default), and b=the number of principal components explaining 99.5% of the variance in the kernel matrix. The output of the program is a set of coordinates representing the average positions of pathways on a 2D map. The x and y axes represent the dimensions of a 2D latent space. The pathway coordinates and corresponding MAGMA P-values were used to build the pathway activity landscape using the kriging interpolation algorithm implemented in the R gstat package.
