These ideas will be implemented to the 1.4.0-dev branch before the official release.
Ideas that are already implemented:
~~Update the make_manifest command so that the sample IDs are determined better. Currently, the
word before the first underscore is set as the sample ID (e.g. 'EXAMPLE'
in EXAMPLE_S1_R1_001.fastq.gz). This works fine in most cases, but gives an error for file names like EXAM_PLE_S1_R1_001.fastq.gz.~~ Done, see b68159a.
Rearrange the arguments for the _artist method to prevent unexpected behaviors. For example, currently using hide_ytexts=True still displays the y-axis tick labels if ymax is also used. Done, see ac1c4fc.
Create a command called summarize for extracting summary statistics (e.g. minimum depth) from FeatureTable[Frequency]. Currently, in order to view summary statistics, you have to create a Visualization file and then open it with other tools (e.g. QIIME 2 View), which is not ideal when you are working in a remote server. Done, see 0b37080.
Update the alpha_rarefaction_plot method to plot lines for all the individual samples but label them by their group variable instead of sample name. The current behavior is either labeling the individual lines by sample name or plotting the lines for group averages. Done, see b07b73a.
Add a new argument called legend_lw to the _artist method. Done, see 8cea3c9.
Update the add_metadata command so that it does not change the sample order after merging. Done, see ec46f80.
Update the add_metadata command to warn when the final metadata contains NaN. Done, see e2858e2.
Update summarize command to output sample IDs and feature IDs. Done, see edecf1e.
Update the _artist method to detect the legend handle so that the legend_lw argument can be interpreted better. Done, see f7682c9.
Add the --verbose option to the summarize command. Done, see 66be20c.
Add the --output_dir option to the collapse command. Done, see 3de7ac3.
Add a new plotting method called heatmap. Done, see f5c4049.
Add cmap_name argument to taxa_abundance_bar_plot method. Done, see 3cfeb7d.
Changed the taxa_abundance_box_plot method to use seaborn.stripplot() instead of seaborn.swarmplot() for plotting data points. Done, see aebd400.
Added to the taxa_abundance_box_plot method the jitter and alpha arguments for setting the aesthetics of data points. Done, see aebd400.
Add seed argument to alpha_rarefaction_plot method so that the result is reproducible. Done, see 62d48f2.
Ideas that will most likely be implemented:
Other ideas:
The Seaborn package is misusing a legend label as a title (https://stackoverflow.com/questions/51579215/remove-seaborn-lineplot-legend-title). This behavior makes the detection of legend title difficult. I made an update (8b642fd) that will fix the issue for the alpha_rarefaction_plot method specifically, but it's not a general solution. I will need to come up with more general solution.
These ideas will be implemented to the
1.4.0-devbranch before the official release.Ideas that are already implemented:
make_manifestcommand so that the sample IDs are determined better. Currently, the word before the first underscore is set as the sample ID (e.g. 'EXAMPLE' in EXAMPLE_S1_R1_001.fastq.gz). This works fine in most cases, but gives an error for file names like EXAM_PLE_S1_R1_001.fastq.gz.~~ Done, see b68159a.Rearrange the arguments for theDone, see ac1c4fc._artistmethod to prevent unexpected behaviors. For example, currently usinghide_ytexts=Truestill displays the y-axis tick labels ifymaxis also used.Create a command calledDone, see 0b37080.summarizefor extracting summary statistics (e.g. minimum depth) fromFeatureTable[Frequency]. Currently, in order to view summary statistics, you have to create a Visualization file and then open it with other tools (e.g. QIIME 2 View), which is not ideal when you are working in a remote server.Update theDone, see b07b73a.alpha_rarefaction_plotmethod to plot lines for all the individual samples but label them by their group variable instead of sample name. The current behavior is either labeling the individual lines by sample name or plotting the lines for group averages.Add a new argument calledDone, see 8cea3c9.legend_lwto the_artistmethod.Update theDone, see ec46f80.add_metadatacommand so that it does not change the sample order after merging.Update theDone, see e2858e2.add_metadatacommand to warn when the final metadata contains NaN.UpdateDone, see edecf1e.summarizecommand to output sample IDs and feature IDs.Update theDone, see f7682c9._artistmethod to detect the legend handle so that thelegend_lwargument can be interpreted better.Add theDone, see 66be20c.--verboseoption to thesummarizecommand.Add theDone, see 3de7ac3.--output_diroption to thecollapsecommand.Add a new plotting method calledDone, see f5c4049.heatmap.AddDone, see 3cfeb7d.cmap_nameargument totaxa_abundance_bar_plotmethod.Changed theDone, see aebd400.taxa_abundance_box_plotmethod to useseaborn.stripplot()instead ofseaborn.swarmplot()for plotting data points.Added to theDone, see aebd400.taxa_abundance_box_plotmethod thejitterandalphaarguments for setting the aesthetics of data points.AddDone, see 62d48f2.seedargument toalpha_rarefaction_plotmethod so that the result is reproducible.Ideas that will most likely be implemented:
Other ideas:
alpha_rarefaction_plotmethod specifically, but it's not a general solution. I will need to come up with more general solution.