create 3d Geometry by given TADs — createTADGeometries • geomeTriD

Create a 3d Geometry by given TADs for target 3d positions.

createTADGeometries(
  tad,
  targetObj,
  type = "sphere",
  name = "TAD_",
  tag = "TAD",
  alpha = 0.2,
  lwd = 3,
  ...
)

Arguments

tad: The TAD. An object of GRanges.
targetObj: The GRanges object with mcols x0, y0, z0, x1, y1, and z1
type: The Geometry type. default is sphere. Possible types are sphere or segment.
name: The prefix for the name of the geometries.
tag: The tag used to group geometries.
alpha: alpha value. default is 0.2
lwd: line width for segment.
...: other properties.

Value

threeJsGeometry objects

Examples

library(GenomicRanges)
obj <- readRDS(system.file("extdata", "4DNFI1UEG1HD.chr21.FLAMINGO.res.rds",
  package = "geomeTriD"
))
tjg <- view3dStructure(obj, renderer = "none")
pc <- pointCluster(as.data.frame(mcols(obj)))
#> eps is set to 1.92420018162681e-06
tads <- split(obj, pc$cluster)
tads <- tads[names(tads)!="0"] # cluster 0 is noise
tads <- unlist(range(GRangesList(tads)))
backbone <- extractBackbonePositions(tjg)
tad_geometries <- createTADGeometries(tads, backbone)
threeJsViewer(tjg, tad_geometries)