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Changelog

Version 2.1.0 (2016-08-28)

  • Improved algorithm for generating signatures based on significantly enriched gene sets, and introduced a new parameter, sig_min_genes to specify the minimum number of genes in each signature. Effectively, this makes gene set enrichment analysis and signature generation more independent of each other, and results in more coherent signatures (i.e., genes in a signature should have more similar expression patterns with the new algorithm).
  • Improved the "Installing GO-PCA" section of the documentation. The section now includes accurate instructions for Windows and Mac OS X.
  • Reduced the verbosity of GO-PCA output. The old verbosity can be restored by passing verbose=True to GO-PCA, or by running the go-pca.py script with the -v option.
  • Changed data structure used for representing signature matrices (GOPCASignatureMatrix now inherits from genometools.expression.ExpMatrix).
  • Added simplified functions for plotting heatmaps of signature matrices and signature genes to the Python API: GOPCASignatureMatrix.get_figure() and GOPCASignature.get_figure().

2.1.1 (2016-09-04)

  • Travis deploy step now generates and uploads wheels.
  • Fixed bug in GOPCASignatureMatrix.filter_collection_signatures().

2.1.2 (2016-09-04)

  • Changed genometools dependency to version 2.0.2.

2.1.3 (2016-09-04)

  • Renamed GOPCA.simple_init() to simple_setup().

2.1.4 (2016-10-06)

  • Modified GOPCASignature.get_figure() call signature.

Version 2.0.0 (2016-08-01)

  • Generalized the API to support multiple "configurations" as input. Each configuration (GOPCAConfig) consists of a set of GO-PCA parameters (GOPCAParams), a list of gene sets (genometools.basic.GeneSetCollection), and, optionally, a gene ontology (genometools.ontology.GeneOntology). GO-PCA is performed independently for each configuration, and the signatures generated are merged into a single signature matrix. The old way of configuring GO-PCA is available as GOPCA.simple_setup().

Version 2.0.1 (2016-08-16)

  • Some bugfixes

Version 1.2.0 (2016-07-26)

  • Full Python 3.5 support (on top of Python 2.7)
  • New Python API for running GO-PCA, accessing results and generating figures
  • Integrated code with genometools 2.0
  • Cleaned up code
  • Added tests (using py.test)
  • Switched to plotly as plotting backend (dropped matplotlib)

1.2.1 (2016-07-26)

  • Updated changelog, fix version number in documentation

1.2.4 (2016-08-04)

  • Fixed bug that made it impossible to run GO-PCA from the command line (go-pca.py)

1.2.5 (2016-08-05)

  • Fixed a bug that prevented the Gene Ontology file from being loaded when running GO-PCA from the command line (go-pca.py)

Version 1.1.3 (2016-02-23)

Version 1.1.2 (2016-02-04)

  • Fixed a bug in the local filter that resulted in incorrect filtering

Version 1.1.0 (2016-02-02)

  • Restructured the documentation (work still ongoing).
  • The "GO annotation file" is now more accurately being referred to as "gene set file"
  • Modified file format for supplying gene sets (added a "description" column)
  • GO-PCA is intended to work with arbitrary gene sets, and the code now reflects this as well (parameter names, variable names, etc.)
  • Added support for INI-style GO-PCA configuration file ("go-pca.py -c ...")
  • Improved documentation of command-line pamaraters ("go-pca.py --help")
  • Improved support for config and result MD5 hash values (they are now shown by "gopca_print_info.py")

Version 1.1rc12

  • Reorganized internal class structure (see GOPCARun in run.py)
  • Added Unicode support
  • Added gopca_print_info.py script to quickly inspect GO-PCA output data

Version 1.1rc10

  • Fixed a bug that occurred when no ontology file is given.

Version 1.1rc9

"Visible" changes:

  • Changed the names of some command line arguments.
  • Added/improved documentation of command line parameters for all scripts.
  • Changed the sphinx html documentation theme to bootstrap ("sphinx-bootstrap-theme").

Internal changes:

  • Improved code documentation.
  • The GO-PCA parameters disable_local_filter and disable_global_filter are now called no_nocal_filter and no_global_filter, respectively.
  • The expression matrix is now represented using the ExpMatrix class from the genometools package.
  • Shared parameter for plotting scripts are now obtained using functions from the plotting.params module (this greatly reduced code redundancy).
  • Loggers are no longer class members, and are instead defined as global variables within each module. This is consistent with the recommended naming scheme that uses logging.getLogger(__name__), thus naming a logger after the module. This helped to simplify the class structures.