These ideas will be implemented to the 1.5.0-dev branch before the official release.
Ideas that are already implemented:
Update the alpha_diversity_plot method to accept metadata. Done, see 290cebf.
Update the alpha_diversity_plot method to accept as input a SampleData[AlphaDiversity] file (e.g. shannon_vector.qza) instead of the Visualization file from qiime diversity alpha-group-significance (e.g. shannon_group-significance.qzv). Done, see 290cebf.
Add legend_title option to _artist method. Done, see f37d0cc.
Update beta_3d_plot method to have legend title. Done, see f37d0cc.
Update beta_parallel_plot method to have legend title. Done, see 0995a40.
Add cmap_name argument to barplot method. Done, see a23e8bc.
Fix a bug in the ordinate method when using both the biplot=True and where arguments with the following error message: The eigenvectors and the descriptors must describe the same samples. Done, see eecc1b0.
Update the taxa_abundance_box_plot method to accept metadata as input. Done, see a573e00.
Update the taxa_abundance_box_plot method to add legend title when the hue argument is provided. Done, see 1478119.
Add the hue_order argument to the heatmap method. Done see 39ece11.
Change the name of the where argument to hue for the heatmap method. Done see 39ece11.
Update the taxa_abundance_bar_plot and taxa_abundance_box_plot methods to sort the samples by their name. Done, see 3ebc9d9.
Add a new method called regplot for plotting relative abundance data and a linear regression model fit from paired samples for the given taxon. Done, see 3352737.
Package dokdo with setuptools. Done, see 7e2896a.
Update the make-manifest command to output the absolute file path instead of the relative file path. Done, see d3c4b41.
Add the prepare-lefse command for creating a text file which can be used as input for the LEfSe tool. Done, see 54488a7.
Retire the merge_metadata command. Done, see a87b020.
These ideas will be implemented to the
1.5.0-dev
branch before the official release.Ideas that are already implemented:
Update theDone, see 290cebf.alpha_diversity_plot
method to accept metadata.Update theDone, see 290cebf.alpha_diversity_plot
method to accept as input aSampleData[AlphaDiversity]
file (e.g.shannon_vector.qza
) instead of the Visualization file fromqiime diversity alpha-group-significance
(e.g.shannon_group-significance.qzv
).AddDone, see f37d0cc.legend_title
option to_artist
method.UpdateDone, see f37d0cc.beta_3d_plot
method to have legend title.UpdateDone, see 0995a40.beta_parallel_plot
method to have legend title.AddDone, see a23e8bc.cmap_name
argument tobarplot
method.Fix a bug in theDone, see eecc1b0.ordinate
method when using both thebiplot=True
andwhere
arguments with the following error message:The eigenvectors and the descriptors must describe the same samples
.Update theDone, see a573e00.taxa_abundance_box_plot
method to accept metadata as input.Update theDone, see 1478119.taxa_abundance_box_plot
method to add legend title when thehue
argument is provided.Add theDone see 39ece11.hue_order
argument to theheatmap
method.Change the name of theDone see 39ece11.where
argument tohue
for theheatmap
method.Update theDone, see 3ebc9d9.taxa_abundance_bar_plot
andtaxa_abundance_box_plot
methods to sort the samples by their name.Add a new method calledDone, see 3352737.regplot
for plotting relative abundance data and a linear regression model fit from paired samples for the given taxon.PackageDone, see 7e2896a.dokdo
withsetuptools
.Update theDone, see d3c4b41.make-manifest
command to output the absolute file path instead of the relative file path.Add theDone, see 54488a7.prepare-lefse
command for creating a text file which can be used as input for the LEfSe tool.Retire theDone, see a87b020.merge_metadata
command.Ideas that will most likely be implemented:
Other ideas: