Skip to content

Round and Round

Compare
Choose a tag to compare
@whitews whitews released this 20 May 16:54
· 871 commits to master since this release
0.6.1
be41afd

New features:

  • Experimental support for exporting FlowJo 10 workspace files (limited to single sample groups)
  • Added support for FlowJo 10 biex transform
  • Added inverse transform methods for most transformations
  • implement ignore_transforms option for parsing FJ10 workspaces
  • Sample.apply_transform supports customized transforms per channel via dictionary
  • Create Sample instances from Pandas DataFrame w/MultiIndex columns
  • Sample: store original events unprocessed

API changes:

  • Sample: added attributes scatter_indices & time_index
  • Sample: apply_transform method now has option to include scatter channels
  • GatingStrategy: get_gate_ids now returns a list of tuples containing the gate ID & list of ancestors (gate path)
  • GatingStrategy: new method get_root_gates for ...
  • GatingStrategy: simplify GatingStrategy methods for retrieving gates,
  • GatingStrategy: added new convenience method get_child_gates
  • Session: new method get_group_comp_matrices
  • Session: all method arguments referencing a sample group name are now consistent ('group_name')
  • Session: new method to get all gate IDs & paths for a sample
  • Session: new method get_group_transforms for retrieving group transformations
  • Session: new method export_wsp for exporting a sample group's gating strategy as a FlowJo 10 workspace
  • Session: new methods for retrieving Sample specific comp matrices & transforms for a group
  • Session: new method for retrieving gated events for a Sample
  • Compensation utility functions moved to FlowUtils
  • make sample utils functions public
  • expose calculate_extent function for flowkit-extras

Bug fixes:

  • Clearer error message when requesting sub-sampled events from get_channel_data when Sample has not been sub-sampled
  • Fixed issue where gain was incorrectly applied to time channel data
  • Allow re-use of gates on different branches at any level
  • Applying re-used gates requires the Gate instance to know the full path
  • Fixed plot_scatter for cases where the event arrays are empty
  • Session.get_group_samples() now only returns loaded samples

Documentation:

  • Added more docstrings for Sample, Session, Transform methods
  • Updated tutorial notebooks
  • Added notebook for calculating mean fluorescence intensity (MFI) per channel for gated populations

Dependencies:

  • Support for Python 3.8
  • Removed MulticoreTSNE dependency
  • Removed sklearn dependency
  • Most transform implementations moved to FlowUtils
Assets 2
Loading