access community plugins through artifact API?

Awesome job!
I don't know if this is possible, but can plugins like this be accessed through the artifact API?

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I got a small workaround going for making Krona plots using the python API. It's not using this plugin, but I might as well share it here, in case anybody else is trying to do this. It's a bit hacky, since it requires saving every sample as a .txt in a format that's acceptable for KronaTools, and then passing all of them to KronaTools with a subprocess.
You need to have KronaTools installed! Releases · marbl/Krona · GitHub

DF = taxa.methods.collapse(
    qiime2.Artifact.load(Dir + 'FeatTable.qza'),
    qiime2.Artifact.load(Dir + 'FeatTax.qza'),
Params = ["ktImportText", '-o', Dir + 'Krona.html']  # String list to pass to subprocess later
os.mkdir(Dir+'Temp')  # Folder to store .txt files for each sample
for i in range(len(DF)):
    Row = DF.iloc[i:i + 1]  # get row for the Nth sample
    Row = Row.loc[:, (Row != 0).any(axis=0)]  # remove columns that are 0
    NewDF = [i.split(';') for i in Row.columns]  # Get a list of the column names with Row.columns, and split it into a list of lists using ; as the delimiter.
    NewDF = pd.DataFrame(NewDF)  # When turning a list of lists into a df, each sublist becomes a column. This way we get 7 columns, corresponding to each level of taxonomy
    NewDF.index = Row.iloc[0].tolist()  # Turn the row of values into the index of the new DF
    NewDF.to_csv(Dir+'Temp/' + Row.index[0] + '.txt', sep='\t', header=False, index=True)  # Save. Row.index[0] is the sample name.
    Params.append(Dir + 'Temp/' + Row.index[0] + '.txt')  # Add the location of the .txt to the parameters[*Params])

Hi @MaxEdge, welcome to the QIIME 2 Forum!

It shouldn't be a problem at all to access q2-krona through the artifact API if you have the plugin installed in your QIIME 2 environment. You would just access this in the same way you would other plugins. There's generally no difference between the plugins that are distributed along with QIIME 2 and community plugins, aside from how they're distributed. Have you run into issues? If so, share some details and we'll be happy to try to help.


Hey, thanks for responding!
Unless I'm doing something wrong, I believe the command should be


But I'm getting

AttributeError: module 'qiime2.plugins.krona.methods' has no attribute 'plot'
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I don't have q2-krona installed right now so I can't test this myself, but could you try calling the following:


I swapped methods for actions there.

In QIIME 2, there are three types of Actions: Methods, Visualizers, and Pipelines. plot sounds like a Visualizer to me (but it could also be a Pipeline), so it won't be accessible under qiime2.plugins.krona.methods, but should be under qiime2.plugins.krona.visualizers, or under qiime2.plugins.krona.actions, where you can find all three action types. I tend to call actions via qiime2.plugins.krona.actions in the ArtifactAPI because all actions are accessible there, so I don't necessarily have to know what type of action I'm calling when I call it.

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Oh, I see. I didn't realize there were different actions, and assumed they all used 'methods'. Indeed, it is a visualizer, and must be called as such:


And now it works.
Thanks a lot!


Fantastic! Thanks for letting me know!

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