flotilla: v0.2.5 (March 3rd, 2015)

This is a patch release, with non-breaking changes from v0.2.4. This includes many changes and bugfixes. Upgrading to this version is highly recommended.

• Added data structure and functions for calculating gene ontology enrichment in flotilla.data_model.Study.go_enrichment, using the data structure flotilla.gene_ontology.GeneOntologyData

• New function flotilla.data_model.Study.plot_expression_vs_inconsistent_splicing() shows the percent of splicing events in single cells that are inconsistent with the pooled samples. Has the option to choose an expression cutoff.
• Add options to flotilla.data_model.Study.plot_pca and flotilla.data_model.Study.interactive_pca:
  • Keyword argument color_samples_by will take a column name from the metadata DataFrame, to color samples by different columns in the metadata.
  • Keyword argument scale_by_variance is a boolean which when True (default) will scale the x and y axes by the explained variance of their individual principal components (PC1 for x and PC2 for y). If False, then the axes are the same scale, by the variance in PC1. Often this will "squish" down the samples in the y-axis.

• flotilla.data_model.Study.plot_classifier returns a flotilla.visualize.predict.ClassifierViz object
• Multi-index columns for data matrices are no longer supported
• Modalities are now calculated using Bayesian methods
• flotilla.data_model.Splicing._subset_and_standardize now doesn't fill NAs with the mean Percent spliced-in/Psi/\Psi score for the event, but rather replaces NA with the value 0.5. Then, all values for that event are transformed with arc cosine so that all values range from -\pi to +\pi and are centered around 0.

• Fixed issue with flotilla.data_model.Study.tidy_splicing_with_expression and flotilla.data_model.Study.filter_splicing_on_expression which had an issue with when the index names are not "miso_id" or "sample_id".
• Don't cache flotilla.data_model.BaseData.feature_renamer_series, so you can change the column used to rename features

• Add link to PyData NYC talk
• Add scrambled dataset with ~300 samples and both expression and splicing
• Fix build status badge in README
• Removed auto-call to %matplotlib inline call within flotilla.visualize because it messes up the make lint call and it's dishonest to the user to be messing with their IPython under the hood. It's possible they don't want the plotting to be inline, but rather in a separate X-window as specified by their $DISPLAY environment variable.
• Reformatted all code to pass make lint and make pep8, and these standards will be enforced for all future enhancements.
• Add Gitter chat room badge to README