| -random 4,7 | Create a random matrix of the given size (rows & columns). |
| -negate | Change the sign of the matrix. |
| -invert | Invert by LU decomposition. |
| -svd | Invert by singular value decomposition. |
| -window 5 | Window over which to do permutations for linear sorting. |
| -preference -10 | Homogenous preference for clustering. |
| -verbose 7 | Verbosity of output. |
| -ln_1_R | Use the -ln(1-R) conversion of the input matrix. |
| -lambda 0.6 | Damping factor for clustering (default 0.5). |
| -datatype b | Force writing of a new data type. |
| -scale 3 | Scale the image (must be an integer). |
| -color | Convert to a heat map. |
| -vector file.dat | Input a vector to multiply with the matrix. |
| -outvector file.dat | Output the vector. |
| -outimage file.img | Output the matrix as an image. |