Interactive 3D plot of epigenetic data or single cell data

The geomeTriD (Three-Dimensional Geometry) Package provides interactive 3D visualization of chromatin structures using the WebGL-based three.js or the rgl rendering library. It is designed to identify and explore spatial chromatin patterns within genomic regions. The package generates dynamic 3D plots and HTML widgets that integrate seamlessly with Shiny applications, enabling researchers to visualize chromatin organization, detect spatial features, and compare structural dynamics across different conditions and data types.

See also

Useful links:

• https://github.com/jianhong/geomeTriD

• Report bugs at https://github.com/jianhong/geomeTriD/issues

Author

Maintainer: Jianhong Ou jou@morgridge.org (ORCID)

Authors:

• Kenneth Poss kposs@morgridge.org [funder]

Examples

if(interactive()){
  ## quick start from a simple data
  library(geomeTriD)
  set.seed(123)
  obj <- GRanges("1", IRanges(seq.int(10), width = 1),
                  x = sample.int(10, 10),
                  y = sample.int(10, 10),
                  z = sample.int(10, 10)
                )
  feature.gr <- GRanges("1", IRanges(c(3, 7), width = 3),
                        label = c("gene1", "gene2"),
                        col = c("red", "blue"),
                        type = "gene"
  )
  view3dStructure(obj, feature.gr,
                  renderer = "threejs",
                  coor_mark_interval = 5, coor_tick_unit = 2
  )
}