Ideas for the next Dokdo version (1.6.0)

[sbslee]

These ideas will be implemented to the 1.6.0-dev branch before the official release.

Ideas that are already implemented:

• Fix typo for the add-metadata command. Done, see 496c06e.
• Fix bug with the heatmap() method giving the FloatingPointError: NaN dissimilarity value. error when sample-filtered metadata is provided and the metric='correlation' argument is used. The error is related to this Stack Overflow post where more than one columns "are all zeros, and have no variation at all, making it return nan with correlation". Done, see 6dfa39c.
• Add centered log-ratio (CLR) transformation as a normalization option to the heatmap() method. Done, see 1927cbe.
• Update the heatmap() method to support kwargs that are passed to the seaborn.heatmap() method. Done, see 39da3d0.
• Add a new method called pname() that returns a prettified taxon name. Done, see 4340c70.
• Update the prepare-lefse command to output more informative taxa name than just underscores (e.g. __ or g__). Note that this issue was also raised in this post from the QIIME 2 Forum. Done, see 61dfb2c.
• Update the addpairs() method to accept additional keyword arguments. Done, see 099f961.
• Add a new method called wilcoxon() that computes p-value from the Wilcoxon Signed-rank test. Done, see d05a449.
• Add a new method called num2sig() that converts a p-value to significance annotation. Done, see 92d318b.
• Update addpairs() to support more than two boxes. Done, see 29759ff.
• Add a new method called mannwhitneyu() that computes p-value from from the Mann–Whitney U test. Done, see 10bfd3d.
• Fix bug with the alpha_diversity_plot() method only recognizing an Artifact file, and not an Artifact object, as input. Done, see dc7275e.
• Update the alpha_diversity_plot() method to display sample size in the x-axis. Done, see 1e981a5.
• Update the summarize command to support FeatureData[Sequence]. Done, see c220a31.
• Update the summarize command to support FeatureData[AlignedSequence]. Done, see 8344201.
• Update the summarize command to support the -v/--verbose option. When this option is used, the command will only output the first five records. Done, see 8344201.
• Fix bug with the heatmap() method giving an error when one of the metadata columns has only zeros. Done, see 28b4674.
• Fix bug with the heatmap() method giving an error when using normalize='log10'. Note that this bug was introduced during 1.6.0-dev (1927cbe specifically). Done, see 659fe63.
• Update the heatmap() method to support two grouping variables instead of just one. Done, see 0440fbb.

Ideas that will most likely be implemented:

Other ideas:

[IrshadUlHaq1]

Great work and an excellent resource. Would be nice to incorporate how to do NMDS with QIIME2 generated distances matrices. Also, applying statistics on those taxa box plots would save a lot of time.

[sbslee]

@IrshadUlHaq1, thanks for the kind words and the ideas! I will look into it.