lpca performs length principal components.
usage: lpca [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 |
This is an experimental feature. We are currently validating and writing a paper about it.
Perform length principal components analysis (“length PCA”). Length PCA takes the special structure of phylogenetic placement data into account. Consequently, it is possible to visualize the principal component eigenvectors, and it can find consistent differences between samples which may not be so far apart in the tree. Length PCA is similar to epca but is invariant to edge subdivision on the reference tree where edge PCA is invariant to branch length. Running this command produces the following files for a run with out prefix set to out:
The --som flag triggers a Support Overlap Minimization (SOM) rotation of the principal components. Setting this value to n triggers a rotation of the first n principal component vectors such that the overlap in support (non-zero vector entries) between the vectors is minimized. This can make the projections easier to interpret from a biological perspective, but care should be taken not to rotate noise into more meaningful components (a good rule of thumb is not to rotate vectors with less than 10% of the variance).
Acceptable values are 0 (no rotation; the default), 2 or 3. Looking at the output from the non-rotated principal components can help you determine what is most appropriate here. If 2 or 3 are specified, the follows files will also be output:
See the splitify documentation for information about the --kappa flag.