:tocdepth: 3

.. _guppy_pmlpca:

======
pmlpca
======

`pmlpca` performs poor-man's length principal components.

::

  usage: pmlpca [options] placefiles

Options
=======

--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