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matsen / pplacer

Phylogenetic placement and downstream analysis
http://matsen.fredhutch.org/pplacer/
GNU General Public License v3.0
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`guppy pca` -> `guppy epca` #221

Closed matsen closed 11 years ago

matsen commented 12 years ago

ePCA = edge PCA

metasoarous commented 12 years ago

We should also change the default output extension conventions for increased clarity. The way that we talk about these things has changed a bit, in some part due to the introduction of our SOM (support overlap minimization) rotations.

.rot -> we describe as a transform (and is easy to confuse with a som rotation) .trans -> we describe as a projection

So, instead, how about we use

.trans for the eigenvalues and eigenvector output (currently .rot); .som for their som rotation, and; .proj for the projection of the samples into coordinate space (currently .trans)

metasoarous commented 12 years ago

This issue is being hijacked...

I'm going to change pca to epca, modify the above mentioned extensions, and implement the SOM rotations as one issue/branch. Given that (excepting the subcommand name) these modifications are related to SOM, it makes sense to wrap everything up this way.

In addition to the afore mentioned extensions, the .som.xml extension will be the fattened colored tree output of the rotated components.