Plots the concordances of each replicate in each experiment condition. A concordance can be understood as a confidence in a genomic position's assigned compartment. Mathematically, it is the log ratio of a genomic position's distance to each compartment's centroid, normalized by the distance between both centroids, and min-maxed to a [-1,1] interval.

plotConcordances(
  object,
  chromosome,
  xlim = NULL,
  threshold = 0.05,
  points = FALSE
)

Arguments

object

A HiCDOCDataSet.

chromosome

A chromosome name or index in chromosomes(object).

xlim

A vector of the minimum and maximum positions to display. If NULL, displays all positions. Defaults to NULL.

threshold

Significance threshold for the compartment changes. Defaults to 0.05.

points

Whether or not to add points to the concordances. Defaults to FALSE.

Value

A ggplot.

Examples

data(exampleHiCDOCDataSetProcessed) plotConcordances(exampleHiCDOCDataSetProcessed, chromosome = 1)