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@whitews whitews released this 04 Jul 03:01
· 1047 commits to master since this release
0.5.0
cd4d40f

New features:

  • GatingStrategy & Session classes now support re-using gate IDs in different gate hierarchy branches (i.e. having a child gate "IFNg+" under both a "CD4+" and "CD8+" gate)
  • Added support for FlowJo 10 ellipsoid gates
  • Plotting of gates in Session class now plots only events from the parent gate
  • Added plotting of Quadrant gates
  • Added bokeh hover tool to scatter plots
  • Re-enabled multiprocessing by default for faster processing of gates in a Session
  • Updated plot colormap for better contrast with gate boundaries

API changes:

  • Major cleanup of public/private modules for cleaner API
  • New Quadrant class for cleaner API when creating QuadrantGate instances
  • New wsp_transforms module containing FlowJo specific Transform sub-classes
  • GatingStrategy, Session - added get_transform and get_comp_matrix methods
  • GatingStrategy, Session - added gate_path kwarg for ambiguous gates in get_gate & get_gate_indices
  • Session: add sample_id option to analyze_samples to process a single Sample
  • Session: added ignore_missing_files option to import_flowjo_workspace method for suppressing warnings about missing FCS files when importing a FlowJo WSP file
  • Gate class - added get_dimension method
  • Sample: rename Sample method to as_dataframe (consistent with Matrix class), & added options to re-order and rename columns in output DataFrame
  • Sample: 'fcs' is no longer the default ID when adding a compensation matrix (it is reserved for the embedded comp matrix from the spill metadata value)
  • Matrix: fluorochromes argument is now optional
  • Matrix: new method as_dataframe to get comp matrix as a Pandas DataFrame
  • Dimension: 'uncompensated' is now the default value when creating Dimension instances

Bug fixes:

  • Properly support time channel data when timestep keyword is present in FCS metadata
  • Fixed display of plotted ellipses (corrected angle)
  • Fixed parsing of compensated dimension references in FlowJo WSP files
  • Fixed import of CSV compensation files with commented header
  • Fixed creation of Sample instances from Pandas DataFrame
  • Fixed parsing of FlowJo gate IDs for some WSP variants

Documentation:

  • Documentation now on ReadTheDocs
  • Many more docstrings for classes and methods
  • Added contribution guidelines
  • New tutorial notebook to demonstrate loading of FlowJo workspaces & programmatically replicating the gating strategy
  • New example notebook showing compensation and Matrix class usage
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