Changelog

1.16.0 (2022-12-27)

Add new argument palette to taxa_abundance_box_plot() method.
#51: Fix bug in clustermap() method where color labels disappeared when flip=True.

Update 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 pname() method.
Add new method group_correlation_heatmap().

#39: Add new argument palette to beta_2d_plot() and beta_3d_plot() methods so that users can control categorical color mapping.
#39: Bring back add_datapoints argument to 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 beta_2d_plot() method. It will be passed to seaborn.scatterplot() method so that users can have more control over various aspects of the output plot.
#41: Fix bug in beta_parallel_plot() method when users provide the ax argument.

#37: Add new methods cross_association_table(), cross_association_heatmap(), and cross_association_regplot().

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

#21: Update the taxa_abundance_bar_plot() method to accept pandas.DataFrame in case the input data was not generated from QIIME 2 (e.g. shotgun sequencing).
#19: Remove the artist_kwargs argument from all the remaining methods:
- denoising_stats_plot()
- alpha_rarefaction_plot()
- alpha_diversity_plot()
- beta_2d_plot()
- beta_3d_plot()
- beta_scree_plot()
- beta_parallel_plot()
- distance_matrix_plot()
- regplot()
- taxa_abundance_box_plot()
- taxa_abundance_bar_plot()
Deprecate the barplot() method.
#22: Rename the heatmap() method to clustermap().
#22: Update the clustermap() method to accept 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.
#22: Add a new main plotting method heatmap().
#24: Update the pname() method to allow returning of more than one tax level.
Deprecate the add_datapoints argument in the taxa_abundance_box_plot() method.

#14, #17: Add the group_order option to the taxa_abundance_bar_plot() method.
Fix a minor bug in the addbiplot() method when feature is ‘Unassigned’.
Deprecate the count-reads command.
#19: Remove the artist_kwargs argument from the following methods:
- ancom_volcano_plot()
- read_quality_plot()

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

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 #10 for more details.

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 #8 for more details.

Updated the following methods:
- _artist()
- alpha_rarefaction_plot()
- taxa_abundance_bar_plot()
- taxa_abundance_box_plot()

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 #2 for more details.

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 #1 for more details.

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.