Plot allele-specific chromatin balance across samples (Fig 4a style)

Source: R/DsASC-class.R

For one or more heterozygous SNPs, plots the proportion of reads mapping to the reference allele in each sample, with binomial confidence intervals. Samples can be coloured by any annotation column (e.g. stimulus).

plotASCBalance(
  dsObj,
  snpIds,
  colorBy = "stimulus",
  orderBy = "cellType",
  minReads = 4,
  sigStats = NULL,
  sigCut = 0.1
)

Arguments

dsObj

A DsASC object.

snpIds

Character vector of snpIds (rownames of the count matrix).

colorBy

Sample-annotation column to colour points by (default "stimulus").

orderBy

Sample-annotation column to order the y axis by (default "cellType").

minReads

Minimum reads to display a sample at a site (default 4).

sigStats

Optional output of calcASCStatistics; significant (fdr < sigCut) sample-site points are drawn solid, others faded.

sigCut

FDR threshold for "significant" shading (default 0.1).

Value

A ggplot object.