Question: Plot relative contact frequencies stratified by distance for a limited region?

Hi, thank you for making and maintaining this very useful software.

I am attempting to plot relative contact frequencies stratified by distance with the function GENOVA::RCP() and its argument bedlist, e.g.,

    bed_rDNA <- data.frame(
        "chromosome" = "XII",
        "start" = 451500,
        "end" = 460800
    )

    quant_RCP_rDNA <- GENOVA::RCP(
        list(c_Q, c_1, c_2),
        bedlist = bed_rDNA
    )

    GENOVA::visualise(quant_RCP_rDNA)

The list supplied to GENOVA::RCP() is made up of three objects (c_Q, c_1, c_2) of class "contacts". These objects are derived from .cool files comprised of only one chromosome: XII. Visualization of the resulting "RCP_discovery" object, quant_RCP_rDNA, shows a plot of frequencies of contacts originating from the region supplied to argument bedlist across all of XII.

However, I'd like to visualize the relative contact frequencies within just the region that makes up bed_rDNA. Is this possible?

Thank you.

robinweide / GENOVA

Question: Plot relative contact frequencies stratified by distance for a limited region? #338