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CHANGELOG.md

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calour changelog

Version 2024.8.31

New features:

  • add shuffler optional parameter and improved data validation for analysis.correlation()

Bug Fixes:

  • Update code and unit tests to work with new version of numpy/pandas/scipy/matplotlib (some of the functions are deprecated in newer versions)
  • Bump requirements for numpy/pandas/scipy/matplotlib/python

Version 2024.8.29

New Features:

  • Support lists for sample_metadata and feature_metadata in Experiment.init()

Bug Fixes:

  • Raise error when plotting a heatmap for an empty experiment

Version 2024.5.30

add mRNAExperiment class for handling rna-seq data. interactive heatmap gene information is via the rna_calour module using Harmonizome server (https://maayanlab.cloud/Harmonizome)

Version 2024.5.16

Bug Fixes:

  • update diff_abundance() to work with numeric columns (previously raised an exception)

Version 2023.4.22

Bug Fixes:

  • update the Experiment.plot() function so works also with matplotlib > 3.7

Version 2022.9.8

Other changes:

  • Add type hints to function return values
  • Create Experiment.info dict and populate with md5s if not provided when creating a new experiment

Other changes:

  • Add type hints to function return values
  • Create Experiment.info dict and populate with md5s if not provided when creating a new experiment

Version 2022.7.1

Incompatible changes:

  • Change default join_metadata_fields() inplace parameter to False
  • In plot_diff_abundance_enrichment(), plot_enrichment(), Replaced enriched_exp_color parameter with labels_kwargs, numbers_kwargs, to enable better control of the barplot labels

Bug Fixes:

  • Fix join_metadata_fields() to use axis='s' by default
  • Fix join_experiments() to update exp.info['sample_metadata_md5'] and exp.info['data_md5']
  • Fix join_experiments() to make field parameter optional, enable joining when field already exists in the experiment, and update the doc
  • Fix join_experiments_featurewise() to make field parameter optional, enable joining when field already exists in the experiment, and update the doc
  • Fix join_metadata() to use axis='s' by default
  • Remove normalization check from filter_by_data()
  • Fix heatmap() to copy the colormap to avoid matplotlib depracation warning (modifying the state of a globally registered colormap)
  • Fix experiment read functions to show by default only the summary and first 5 samples without data/without metadata

Version 2020.8.6

Incompatible changes:

  • Change random_seed to work with numpy.random.default_rng. This may cause different random numbers compared to the old versions using numpy.random.seed().
  • Change parameter names in some functions
  • Rename filter_abundance() to filter_sum(abundance)
  • Other backwards incompatible function API changes and code refactoring.

New features:

  • Add RatioExperiment for working with ratios between two groups of features
  • Add random_seed option to tranforming.permute_data()
  • Add bad_color parameter to heatmap() and derivative functions
  • Add more methods for MS1Experiment
  • Add q-values (correted p-values) to dsfdr and derivative functions. This is manifested in a new feature_metadata field ("qval") for results of diff_abundance() / correlation()
  • improved GUI for qt5 heatmap database enrichment results.
  • Add read_qiime2() function to enable reading of qiime2 feature tables artifacts with the associated representative sequences and taxonomy artifacts (without the need to install qiime2)
  • Add Experiment.validate().
  • Change default color scale in heatmap plot to linear scale for Experiment and log scale for AmpliconExperiment and MS1Experiment.
  • Move to pytest for unit tests and doctests.
  • Add new mechanism to register a function to a class as a method automatically. In order for a function to be registerred to a class, it must be a public function and has type hint of the class type for its first function parameter and return value.
  • Clean and improve API documentation.

Other changes:

  • make scikit-bio an optional dependency (needed only when processing dendrograms)

Version 2019.5.1

  • Add reverse parameter to the sorting functions.
  • Fix minor documentation formatting issues
  • Update installation instruction with conda install from conda-forge
  • Change the column names added to Experiment.feature_metadata after running Experiment.correlation or Experiment.diff_abundance

Version 2018.10.1

  • Add notebook tutorial for calour.training module for classification and regression.
  • Add notebook tutorial for metabolome data analysis
  • Add plot functions in calour.training module
  • Fix a bug in Expriment.aggregate_by_metadata when the number in the data table is overflow the int type.
  • Add CONTRIBUTING.md as guidelines

Version 2018.5.2

  • Add export_html() function to save heatmap as an interactive html heatmap

Version 2018.5.1

  • In calour.training module, added functions to do regression and classification and to visualize their results. SortedStratifiedKFold and RepeatedSortedStratifiedKFold are aslo added for stratified cross validation for regression. They are recommended.