Region flag is not properly handled in arc_plots_compare

[SimonFelder]

Using region argument when comparing arc plots, it only applies to the profile but full length sequence and arcs are still displayed.

[SimonFelder]

Neither are domains in StructureCompareMany

[SimonFelder]

[Psirving]

Thanks Simon, the screenshot helps me a lot.

I don't think StructureCompareMany is affecting this. It looks like those arcs are isolated to your region. I think these two issues are related though. With either plot_arcs_compare or domains there are bars plotted along the x-axis that aren't being clipped to the region. It should be relatively simple to fix. I'll get to it this week or next.

[Psirving]

Scott, Will, and Simon have all run into this issue, so I definitely need to fix something and/or add clarification in the documentation.

rnav.plot_arcs_compare is meant to display two full sequences that do not align positionally. This means that we end up with 3 coordinate systems, that of sequence 1, sequence 2, and of the actual x-axis. It is not obvious to me which of these region should apply to.

In the case where sequence 1 and 2 are the same, rnav.plot_arcs_compare adds extra clutter by showing 2 x-axes and the positional alignment between them. This alignment also removes the space where annotations would otherwise go. For Simon, Will, and Scott's cases, a better solution is to use rnav.plot_arcs, adding both samples to the same axes.

Note: this method will not align sequences or filter interactions for the second sample. I can provide code to do this if needed.

# create the plot with a single sample
plot = rnav.plot_arcs(
    samples=[my_first_sample],
    sequence="ss",
    structure="ss",
    interactions="ringmap",
    profile="shapemap",
    region=(72, 200),
    panels={
        "structure": "top",
        "interactions": "top",
        "profile": "top"
    },
)

# add a second sample to the same axes
plot.plot_data(
    ax=0,
    sequence=my_second_sample.get_data("ss"),
    interactions=my_second_sample.get_data("ringmap"),
    structure=my_second_sample.get_data("ss"),
    profile=my_second_sample.get_data("shapemap"),
    panels={
        "structure": "bottom",
        "interactions": "bottom",
        "profile": "bottom"
    }
)