regionOverlaps — regionOverlaps • epiwraps

A wrapper for visualizing pairwise-wise overlaps across multiple sets of genomic ranges.

Usage

regionOverlaps(
  listOfRegions,
  mode = c("reduced", "pairwise"),
  ignore.strand = TRUE,
  cluster = length(listOfRegions) > 2,
  colorBy = c("overlapCoef", "jaccard"),
  ...,
  returnValues = FALSE,
  color = viridisLite::plasma(100),
  number_color = "black"
)

Arguments

listOfRegions: A named list of two or more (non-empty) `GRanges`
mode: Either 'reduced' or 'pairwise'. 'reduced' first uses `reduce` to get a set of reference regions which are, based on overlap, contained or not in the different sets. It is thus symmetrical. `pairwise` does pairwise overlap between the sets of regions; it is asymmetrical and slower to compute.
ignore.strand: Logical; whether to ignore strand for overlaps (default TRUE).
cluster: Logical; whether to cluster rows/columns
colorBy: Whether to color by 'overlapCoef' (default), or by 'jaccard' index.
...: Passed to pheatmap
returnValues: Logical; whether to return the matrix of requested values instead of plotting.
color: Heatmap colorscale
number_color: Values color

Value

A `Heatmap` showing the overlap coefficient as colors, and the overlap size as values. Alternatively, if `returnValues=TRUE`, a matrix of the requested values.

Examples

# random list of GRanges:
grl <- lapply(c(A=10,B=20,C=30), FUN=function(x){
  GRanges("seq1", IRanges(runif(x,1,1000), width=20))
})
regionOverlaps(grl)