Pathogen-embed

Latest version: v3.1.0

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2.0.0

Major Changes

* Removed seaborn as a dependency in favor of base matplotlib ([13][])
* Set default learning rate for t-SNE to "auto" such that the learning rate scales with the sample size ([12][])

Features

* Add support for multiple alignment and/or distance matrix inputs to `pathogen-embed` ([19][])
* Add optional output from `pathogen-embed` that produces the boxplot figure of Euclidean by genetic distance ([14][])

Bug Fixes

* Display default parameters for subcommands of pathogen-embed ([12][])

[12]: https://github.com/blab/pathogen-embed/pull/12
[13]: https://github.com/blab/pathogen-embed/pull/13
[14]: https://github.com/blab/pathogen-embed/pull/14
[19]: https://github.com/blab/pathogen-embed/pull/19

1.1.2

Bug Fixes

* Fix t-SNE keyword argument error associated with recent versions of scikit-learn ([6][])
* Pass random seed argument from the command line to PCA and MDS implementations ([6][])

[6]: https://github.com/blab/pathogen-embed/pull/6

1.1.1

Bug Fixes

* Fix MDS stress output

1.1.0

Features
* Add stress value dataframe to MDS arguments to relay fitness of the embedding

1.0.0

Major Changes

* Created separate commands for embedding, clustering, and distance matrix creation (pathogen-embed, pathogen-cluster, pathogen-distance) ([2](https://github.com/blab/pathogen-embed/pull/2))

0.1.1

Bug Fixes

* Migrated source code and documentation from [cartography](https://github.com/blab/cartography) to [pathogen-embed](https://github.com/blab/pathogen-embed)

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