CHANGELOG.rst

Changelog

1.16.0 (2022-12-27)

• Add new argument palette to :meth:`taxa_abundance_box_plot` method.
• :issue:`51`: Fix bug in :meth:`clustermap` method where color labels disappeared when flip=True.

1.15.0 (2022-08-23)

• Update :meth:`pname` method to support taxa names that don't have a delimiter such as ASV IDs (e.g. 1ad289cd8f44e109fd95de0382c5b252). Basically, the method will simply return the input name as is.
• Add new argument delimiter to :meth:`pname` method.
• Add new method :meth:`group_correlation_heatmap`.

1.14.0 (2022-06-24)

• :issue:`39`: Add new argument palette to :meth:`beta_2d_plot` and :meth:`beta_3d_plot` methods so that users can control categorical color mapping.
• :issue:`39`: Bring back add_datapoints argument to :meth:`taxa_abundance_box_plot` method to display data points on top of the boxes (note that it was deprecated in 1.11.0 version).
• Add new argument kwargs to :meth:`beta_2d_plot` method. It will be passed to :meth:`seaborn.scatterplot()` method so that users can have more control over various aspects of the output plot.
• :issue:`41`: Fix bug in :meth:`beta_parallel_plot` method when users provide the ax argument.

1.13.0 (2022-04-02)

• :issue:`37`: Add new methods :meth:`cross_association_table`, :meth:`cross_association_heatmap`, and :meth:`cross_association_regplot`.

1.12.0 (2022-02-11)

• :issue:`33`: Update the :command:`make-manifest` command to ignore undetermined FASTQ files.
• :issue:`34`: Update the :meth:`alpha_rarefaction_plot` method to keep 'N/A' values as string instead of NaN.
• :issue:`35`: Update the methods :meth:`alpha_diversity_plot`, :meth:`beta_2d_plot`, and :meth:`beta_3d_plot` to accept :class:`pandas.DataFrame` in case the input data was not generated from QIIME 2 (e.g. shotgun sequencing).
• Update the methods :meth:`beta_2d_plot` and :meth:`beta_3d_plot` to print out the proportions explained instead of embedding them in the PCoA plot.

1.11.0 (2021-08-04)

• :issue:`21`: Update the :meth:`taxa_abundance_bar_plot` method to accept :class:`pandas.DataFrame` in case the input data was not generated from QIIME 2 (e.g. shotgun sequencing).
• :issue:`19`: Remove the artist_kwargs argument from all the remaining methods:
  • :meth:`denoising_stats_plot`
  • :meth:`alpha_rarefaction_plot`
  • :meth:`alpha_diversity_plot`
  • :meth:`beta_2d_plot`
  • :meth:`beta_3d_plot`
  • :meth:`beta_scree_plot`
  • :meth:`beta_parallel_plot`
  • :meth:`distance_matrix_plot`
  • :meth:`regplot`
  • :meth:`taxa_abundance_box_plot`
  • :meth:`taxa_abundance_bar_plot`
• Deprecate the :meth:`barplot` method.
• :issue:`22`: Rename the :meth:`heatmap` method to :meth:`clustermap`.
• :issue:`22`: Update the :meth:`clustermap` method to accept :class:`pandas.DataFrame` in case the input data was not generated from QIIME 2 (e.g. shotgun sequencing). You can now also flip the x and y axes with the flip option.
• :issue:`22`: Add a new main plotting method :meth:`heatmap`.
• :issue:`24`: Update the :meth:`pname` method to allow returning of more than one tax level.
• Deprecate the add_datapoints argument in the :meth:`taxa_abundance_box_plot` method.

1.10.0 (2021-07-06)

• :issue:`14`, :issue:`17`: Add the group_order option to the :meth:`taxa_abundance_bar_plot` method.
• Fix a minor bug in the :meth:`addbiplot` method when feature is 'Unassigned'.
• Deprecate the :command:`count-reads` command.
• :issue:`19`: Remove the artist_kwargs argument from the following methods:
  • :meth:`ancom_volcano_plot`
  • :meth:`read_quality_plot`

1.9.0 (2021-06-07)

• Add publicly available datasets from QIIME 2 for tutorials.
• :issue:`14`: Add the group option to the :meth:`taxa_abundance_bar_plot` method. Using this option will create a bar for each group instead of each sample.

1.8.0 (2021-05-09)

• Updated docstring.
• Moved the official documentation from Wiki page to Read the Docs.

1.7.0 (2021-04-05)

• Added a new command called count-reads which counts the number of sequence reads from FASTQ.

• Updated the summarize command.

• Updated the following methods:

  • taxa_abundance_box_plot()
  • taxa_abundance_bar_plot()
  • distance_matrix_plot()
  • ordinate()
  • barplot()

• See :issue:`10` for more details.

1.6.0 (2021-03-08)

• Added a new method called pname() which returns a prettified taxon name.

• Added a new method called num2sig() which converts a p-value to significance annotation.

• Added a new method called wilcoxon() which performs the Wilcoxon Signed-rank test between two paired groups for a given taxon.

• Added a new method called mannwhitneyu() which performs the Mann–Whitney U test between two groups for a given taxon.

• There have been major changes to the heatmap() method. First, it now supports two grouping variables instead of just one (e.g. hue1 and hue2). Second, it supports the centered log-ratio (CLR) transformation as a normalization option (in addition to log10). Third, it now has kwargs that are passed to the seaborn.clustermap() method (e.g. xticklabels=False). Fourth, the bug giving the FloatingPointError: NaN dissimilarity value. error when sample-filtered metadata is provided and the metric='correlation' argument is used has been fixed. Fifth, the bug giving an error when one of the metadata columns has only zeros has been fixed.

• In addition to heatmap(), the following methods have been updated:

  • addpairs()
  • alpha_diversity_plot()

• Updated the summarize command.

• Updated the prepare-lefse command to output more informative taxa name than just underscores (e.g. __ and g__).

• See :issue:`8` for more details.

1.5.0 (2021-02-03)

• Starting this version, Dokdo is packaged with setuptools.

• There have been major changes to Dokdo CLI.

• Added a new plotting method called regplot().

• Added a new command called prepare-lefse.

• The merge_metadata command has been deprecated.

• Updated the following methods:

  • _artist()
  • alpha_diversity_plot()
  • beta_3d_plot()
  • beta_parallel_plot()
  • barplot()
  • ordinate()
  • taxa_abundance_bar_plot()
  • taxa_abundance_box_plot()
  • heatmap()

• Updated the make_manifest command.

• See :issue:`6` for more details.

1.4.0 (2021-01-09)

• Added a new command called summarize.

• Added a new plotting method called heatmap().

• Updated the following commands:

  • make_manifest
  • add_metadata
  • collapse

• Updated the following methods:

  • _artist()
  • alpha_rarefaction_plot()
  • taxa_abundance_bar_plot()
  • taxa_abundance_box_plot()

• See :issue:`4` for more details.

1.3.0 (2020-12-23)

• Updated the ordinate() method so that the user can now choose to:

  • skip rarefying,
  • provide custom sampling depth for rarefying,
  • provide qiime2.Artifact as input instead of file path, and
  • output PCoAResults % Properties('biplot') as well as PCoAResults.

• Added new plotting methods:

  • beta_scree_plot()
  • beta_parallel_plot()
  • addbiplot()
  • barplot()

• See :issue:`2` for more details.

1.2.0 (2020-12-08)

• The tax2seq command has been deprecated.
• Updated the _artist() method to set the font size of title, labels, etc.
• Added the s argument to the ancom_volcano_plot() method for setting marker size.
• Updated the docstring.
• See :issue:`1` for more details.

1.1.0 (2020-11-23)

• Introduced the addpairs() method.

• The beta_2d_plot_gallery() method has been deprecated.

• Made some changes to the following methods:

  • ordinate()
  • taxa_abundance_bar_plot()
  • taxa_abundance_box_plot()
  • _artist()

• Fixed some bugs.

• Made keyword arguments for the _artist() method more explicit with artist_kwargs.

• Temporary files will be deleted automatically from now on.

• Updated the docstring.

• Plotting methods now accept Artifact and Visualization objects as input.

1.0.0 (2020-11-09)

• Initial release.