Convert list output to an class and split out plot function

Change the return type when summarize_clones=TRUE from a list an S4 object (“CloneSummary”, just “Clones”, not sure on the name). Basically the same thing, except as defined slots: db, vj_group, and eff_threshold.

Also, remove the plot from the return object and have the plot function plotInterVsIntra as a separate exported/documented function that task as input the new S4 object. Same thing you have now, except it just grabs the inter_intra slot from the passed object. This will give users more control over the plotting and remove the weirdness of hiding the plot in the list and it automatically plotting when you run the cloning.

Add a plot function that dispatches to plotInterVsIntra for the new S4 object.

This should be pretty straightforward, as nothing is really changing under the hood, but if you need some help sorting out the details of object-oriented stuff in R (which is really confusing), I’m happy to take care of some of this.

Also, see #8 and #9.

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