pmlpca performs poor-man’s length principal components.
usage: pmlpca [options] placefiles
| --out-dir | Specify the directory to write files to. |
| --prefix | Specify a string to be prepended to filenames. Required. |
| --point-mass | Treat every pquery as a point mass concentrated on the highest-weight placement. |
| --pp | Use posterior probability for the weight. |
| -c | Reference package path. |
| --min-fat | The minimum branch length for fattened edges (to increase their visibility). To turn off set to 0. Default: 0.01 |
| --total-width | Set the total pixel width for all of the branches of the tree. Default: 300 |
| --width-factor | Override total-width by directly setting the number of pixels per unit of thing displayed. |
| --node-numbers | Put the node numbers in where the bootstraps usually go. |
| --gray-black | Use gray/black in place of red/blue to signify the sign of the coefficient for that edge. |
| --min-width | Specify the minimum width for a branch to be colored and thickened. Default is 1. |
| --write-n | The number of principal coordinates to calculate (default is 5). |
| --som | The number of dimensions to rotate for support overlap minimization(default is 0; options are 0, 2, 3). |
| --scale | Scale variances to one before performing principal components. |
| --symmv | Use a complete eigendecomposition rather than power iteration. |
| --raw-eval | Output the raw eigenvalue rather than the fraction of variance. |
| --kappa | Specify the exponent for scaling between weighted and unweighted splitification. default: 1 |
| --rep-edges | Cluster neighboring edges that have splitified euclidean distance less than the argument. |
| --epsilon | The epsilon to use to determine if a split matrix’s column is constant for filtering. default: 1e-05 |