access community plugins through artifact API?

Technical Support
1

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

2

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'),
    level=7
).collapsed_table.view(pd.DataFrame)
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
subprocess.run([*Params])
shutil.rmtree('Qiime/Temp')
5

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.

6

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

qiime2.plugins.krona.methods.plot(
    qiime2.Artifact.load(Dir+'Qiime/FeatTable.qza')
).visualization.save('KRONA.qzv')

But I'm getting

AttributeError: module 'qiime2.plugins.krona.methods' has no attribute 'plot'
7

I don't have q2-krona installed right now so I can't test this myself, but could you try calling the following:

qiime2.plugins.krona.actions.plot

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.

8

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:

qiime2.plugins.krona.visualizers.plot(
        qiime2.Artifact.load(Dir+'Qiime/FeatTable.qza')
    ).visualization.save('KRONA.qzv')

And now it works.
Thanks a lot!

9

Fantastic! Thanks for letting me know!