regionOverlaps

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,
  color = viridis::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

cluster

Logical; whether to cluster rows/columns

color

Heatmap colorscale

number_color

Values color

...

Passed to pheatmap

Value

A `Heatmap` showing the overlap coefficient as colors, and the overlap size as 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)
#> Error in loadNamespace(x): there is no package called 'viridis'