Plot Resolution vs Coverage

Generate a boxplot showing coverage of bins for different bin sizes.

Usage

plotResolutionCoverage(
  pairs,
  bin_sizes = c(1000, 2000, 5000, 10000, 20000, 25000, 50000, 1e+05, 150000, 2e+05,
    250000, 5e+05, 1e+06),
  min_contacts = 1000,
  title = "Coverage by Resolution"
)

Arguments

pairs

A data frame or tibble with columns: read_name, chrom1, pos1, chrom2, pos2.

bin_sizes

Integer vector of bin sizes to test (in base pairs). Default: c(1e3, 2e3, 5e3, 1e4, 2e4, 2.5e4, 5e4, 1e5, 1.5e5, 2e5, 2.5e5, 5e5, 1e6)

min_contacts

Integer minimum number of contacts. Default: 1000.

title

Character title for the plot. Default: "Coverage by Resolution".

Value

A ggplot2 object showing coverage distribution across bin sizes.

Details

Creates a boxplot visualization where each panel represents a bin size, and the distribution shows the number of contacts per bin. This helps visualize how resolution affects coverage across the genome.

Examples

if (FALSE) { # \dontrun{
# Plot coverage for default bin sizes
p <- plotResolutionCoverage(pairs)
print(p)

# Custom bin sizes
p <- plotResolutionCoverage(pairs,
  bin_sizes = c(10000, 50000, 100000, 500000)
)
print(p)
} # }