dcdanko / biobitbot Goto Github PK

Should be applied to:

• Sig plots for metagenomics
• PCA plots

Hello!

I have a suggestion about how to mutually develop code. Could it make sense to develop this code in a separate package instead of a fork of the main tool? I can't think of any functionality that you'd miss out on that way, and it would mean that your code wouldn't diverge from the core MultiQC package..

The documentation on how to do this is a bit lacking, as I haven't done loads of it myself yet, but it's essentially the same concept as in MultiQC_NGI - using setuptools to add new functions, modules, templates and command line options.

The entry points are pretty powerful in this sense. For instance, you could also create your own namespace alongside for the common functions so that other packages can use yours as a dependency. eg:

entry_points = {
    # To tie into core MultiQC execution
    'multiqc.modules.v1': [
        'yourmodule = your_extension.yourmod:MultiqcModule'
    ],
    # Your common functions for others to import into their code
    'yourmodule.functions.v1': [
        'scatter_plot = your_extension.yourfuncs:ScatterPlot'
    ]
},

then someone else's code:

import pkg_resources

pkg_resources.load_entry_point('yourmodule', 'functions.v1', 'scatter_plot')

(I think - this is slightly different from what I do, but hopefully you get the idea)

Your package can essentially be as stand-alone as you like - you can import whatever core functions you want through import multiqc statements and you can export any functions you like using your own entry_points. As long as you add a multiqc entry_point so that your code is triggered when MultiQC runs, it should all tie together.

Does that make sense? What do you think?

Phil

For a given analysis module but different sub-modules on separate tabs?

Box plots should be displayed for all Significant genes.

Some plots would look better if they were side by side.

Particularly volcano and MA

Both the microarray and metagenomic module are collections of plots. It may make sense to refactor the current modules into sets of modules that are run for the specific analysis.

This is similar to how the original MultiQC works but will have to handle files and data sharing within modules differently.