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