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v0.2.5 (March 3rd, 2015)
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@olgabot olgabot released this 04 Mar 22:21
· 2364 commits to master since this release
v0.2.5
2e20564

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.

New features

  • 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

Plotting functions

  • 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.

API changes

  • 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.

Bug fixes

  • 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

Miscellaneous

  • 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
Assets 2