flowcal - Version 1.3.1

Fixed a deprecation issue with Matplotlib.ticker.is_decade

- Python
Published by djhaller about 1 year ago

flowcal - Version 1.3.0

New features: - Added functions that plot violin plots (FlowCal.plot.violin() and FlowCal.plot.violin_dose_response()). [PR335] - Added a new way to save and reuse density gates (FlowCal.gate.density2d() now accepts and returns a bin_mask array). [PR337] - Added channel_labels() method to FCSData objects, which returns $PnS keyword values (i.e., long channel names). [PR323]

API changes: - FlowCal.gate.density2d() now accepts and returns a bin_mask array. [PR337] - All outputs returned by FlowCal.excel_ui.process_beads_table() and FlowCal.excel_ui.process_samples_table() are now OrderedDicts. [PR334]

Other changes: - Migrated Excel engine to openpyxl. [PR325, PR329, 8bcb6072163226bd4eac8373295f4b5c86eee755, 97147912b2d1556669857ddb44622af244424090] - Removed dependency on palettable. [PR328] - Modified macOS install and run scripts to work with both bash and zsh. [f4f055f0830a528416f13f699f4a23fb4becb81e, 067a1ece0d98497abddccdcc9a54140993222e5c] - Refactored FlowCal.plot.hist1d() to permit weights kwarg. [PR333] - FlowCal.mef.get_transform_fxn() now accepts None in mef_channels list. [PR331]

- Python
Published by JS3xton over 5 years ago

flowcal - Version 1.2.2

• Compatibility fixes with matplotlib 3.1.0.
• Installation and usage improvements for macOS.
• FCSData can be used with the pickle module.

- Python
Published by castillohair over 6 years ago

flowcal - Version 1.2.1

Fixed small incompatibility bug with Python 3.7.

- Python
Published by castillohair over 7 years ago

flowcal - Version 1.2.0

• Added compatibility with Python 3.6.
• Added a command line entrypoint: The Excel UI can be called from the command line by entering flowcal.
• Resolved several issues with more recent versions of prerequisite packages.

- Python
Published by castillohair almost 8 years ago

flowcal - Version 1.1.4

• Added compatibility with pandas 0.20.1.
• Improved documentation on installing Anaconda.

- Python
Published by castillohair about 9 years ago

flowcal - Version 1.1.3

• Restored default black edges in histograms when using matplotlib 2.0.0.
• Made histogram sheet from the Excel UI optional.
• Improved error detection of nonsensical error fractions (e.g. 1.5).

- Python
Published by castillohair about 9 years ago

flowcal - Version 1.1.2

Fixed incompatibility with matplotlib 2.0.0.

- Python
Published by castillohair over 9 years ago

flowcal - Version 1.1.1

This version fixes minor bugs and improves compatibility with respect to version 1.1.0.

Bug fixes

• FCSData now loads fcs files successfully when the file contains information on $PnG and $PnV other than numbers.
• Linear gain in specific files generated by FlowJo Collectors Edition is now properly extracted.
• FlowCal.gate.start_end() now behaves as expected when num_end=0.
• plot.scatter3d() now works with matplitlib 1.5.1.

Code improvements

• FlowCal.excel_ui.process_beads_table() and FlowCal.excel_ui.process_samples_table now plot to the standard output when plot_dir is not specified.
• excel_ui.process_beads_table() now contains an additional argument to directly control mef.get_transform_fxn().

- Python
Published by castillohair over 9 years ago

flowcal - Version 1.1.0

High-level changes

• Improved compatibility with different FCS files.
• Improved ability to handle high-resolution FCS data and floating-point data, and transform this data to MEF.
• Logicle scale implemented. This is the new default for plotting.

Important code changes

Gating and plotting

• gate.density2d and all simple plotting functions now include arguments xscale, yscale, and zscale as appropriate, to define the scale of each axis. Valid options are 'linear', 'log', and 'logicle'. All these functions default to logicle.
• Arguments log, xlog, ylog, and zlog in plotting functions are deprecated.

I/O

• FCSData property domain has been deprecated. New function range returns, for each specified channel, the lower and upper bounds as specified by the FCS file.
• FCSData property hist_bin_edges has been deprecated. New function hist_bins allows for dynamic generation of histogram bins using either linear, logarithmic, or logicle scaling.

MEF

• The transformation function returned by get_transform_fxn is now meant to be used with data previously transformed to RFI using transform.to_rfi().
• Functions clustering_gmm and selection_std now allow for rescaling of the data before performing their operations. The default scaling is logicle.
• fit_beads_autofluorescence now uses a model that transforms data from RFI to MEF. Previously, the model was meant to be used to transform data in raw channel numbers to MEF, when using a logarithmic amplifier. The new approach allows for transformation of data taken with linear amplifiers as well.

- Python
Published by castillohair about 10 years ago

flowcal - Version 1.0.0

Changes in Excel UI: - Statistics for beads files, including bead model parameter, detector gain, and others. - User-friendly error reporting for files with low event counts, non-existing files, and acquisition settings of corresponding beads and samples not identical. - Command-line parameters for the Excel UI, which allows the user to batch-process several files, and turn on or off the generation of plots.

Changes in code: - transform.exponentiate() deprecated in favor of transform.to_rfi(), which automatically decides whether to exponentiate the data based on acquisition settings.

Other changes: - Bug when loading files that do not contain a valid $DATE keyword.

- Python
Published by castillohair over 10 years ago

flowcal - Version 1.0 beta 2

Changes in Excel UI: - Titles in density/histogram plots produced by the Excel UI now have the sample ID instead of the file name. - Corrected bug that interfered with the Excel UI's file selection window in OSX.

Other changes: - Earlier versions of some requirements are now supported.

- Python
Published by castillohair over 10 years ago

flowcal - Version 1.0 beta 1

Code changes: - Package name has been officially changed to FlowCal. - Reorganized modules plot and mef.

- Python
Published by castillohair over 10 years ago

flowcal - Version 0.8.1

New feaures: - New Excel interface! - Scripts for easy installation and launch of Excel UI .

Others: - Code style changes. - New unit tests.

- Python
Published by castillohair over 10 years ago

flowcal - Version 0.7.1

New features: - Template excel file, with explanations of fields. - fc now optionally uses palettable for default colors.

Bug fixes: - If using pip, openpyxl 2.0.2 is installed instead of using the last version. This fixes some installation problems.

Others: - Small code style changes - Importing fc imports all the submodules by default.

- Python
Published by castillohair almost 11 years ago

flowcal - Version 0.7

New features: - Full support for FCS2.0 and 3.0 files.

Bug fixes: - Changed color of gate in plots to increase contrast. - Solved bug in acquisition time calculation in windows.

- Python
Published by castillohair almost 11 years ago

flowcal - Version 0.6

Improvements in the excel input/output script: - Channels in which statistics and plots can be calculated can now be specified in the input excel spreadsheet. - Channels in which MEF transformations should be done can now be specified. - Acquisition time is now reported as one of the statistics.

Other new features: - Bar plotting functions. - Fixed ellipse gate. - Acquisition time reported via .acquisition_time property in the FCSData object.

- Python
Published by castillohair almost 11 years ago

flowcal - First release!

- Python
Published by castillohair almost 11 years ago