Changelog
1.16.0 (2022-12-27)
Add new argument
palette
totaxa_abundance_box_plot()
method.#51: Fix bug in
clustermap()
method where color labels disappeared whenflip=True
.
1.15.0 (2022-08-23)
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
topname()
method.Add new method
group_correlation_heatmap()
.
1.14.0 (2022-06-24)
#39: Add new argument
palette
tobeta_2d_plot()
andbeta_3d_plot()
methods so that users can control categorical color mapping.#39: Bring back
add_datapoints
argument totaxa_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
tobeta_2d_plot()
method. It will be passed toseaborn.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 theax
argument.
1.13.0 (2022-04-02)
#37: Add new methods
cross_association_table()
,cross_association_heatmap()
, andcross_association_regplot()
.
1.12.0 (2022-02-11)
#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()
, andbeta_3d_plot()
to acceptpandas.DataFrame
in case the input data was not generated from QIIME 2 (e.g. shotgun sequencing).Update the methods
beta_2d_plot()
andbeta_3d_plot()
to print out the proportions explained instead of embedding them in the PCoA plot.
1.11.0 (2021-08-04)
#21: Update the
taxa_abundance_bar_plot()
method to acceptpandas.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 toclustermap()
.#22: Update the
clustermap()
method to acceptpandas.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 theflip
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 thetaxa_abundance_box_plot()
method.
1.10.0 (2021-07-06)
1.9.0 (2021-06-07)
Add publicly available datasets from QIIME 2 for tutorials.
#14: Add the
group
option to thetaxa_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 #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
andhue2
). Second, it supports the centered log-ratio (CLR) transformation as a normalization option (in addition tolog10
). Third, it now haskwargs
that are passed to theseaborn.clustermap()
method (e.g.xticklabels=False
). Fourth, the bug giving theFloatingPointError: NaN dissimilarity value.
error when sample-filtered metadata is provided and themetric='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.__
andg__
).See #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 #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 #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, andoutput
PCoAResults % Properties('biplot')
as well asPCoAResults
.
Added new plotting methods:
beta_scree_plot()
beta_parallel_plot()
addbiplot()
barplot()
See #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 theancom_volcano_plot()
method for setting marker size.Updated the docstring.
See #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 withartist_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.