Plot GRanges xyz data in 2d or 3d — view3dStructure • geomeTriD

Plot GRanges xyz data with grid or rgl package.

view3dStructure(
  obj,
  feature.gr,
  genomicSigs,
  region,
  signalTransformFun = function(x) {
     log2(x + 1)
 },
  k = 3,
  renderer = c("rgl", "threejs", "none"),
  lwd.backbone = 2,
  col.backbone = "gray",
  lwd.maxGenomicSigs = 8,
  reverseGenomicSigs = TRUE,
  col.backbone_background = if (k == 2) "gray70" else c("gray30", "darkred"),
  alpha.backbone_background = 0.5,
  lwd.gene = 3,
  coor_mark_interval = 5e+05,
  col.coor = "black",
  show_coor = TRUE,
  coor_tick_unit = 50000,
  label_gene = TRUE,
  col.tension_line = "black",
  lwd.tension_line = 1,
  length.arrow = unit(abs(diff(obj$x))/20, "native"),
  safe_text_force = 3,
  square = TRUE,
  cluster3Dpoints = FALSE,
  ...
)

Arguments

obj: GRanges object with mcols x, y, and/or z
feature.gr: The annotation features to be added. An object of GRanges.
genomicSigs: The Genomic signals. An object of GRanges with scores or an object of track.
region: A GRanges object with the region to be plot.
signalTransformFun: The transformation function for genomic signals.
k: The dimension of plot. 2: 2d, 3: 3d.
renderer: The renderer of the 3D plots. Could be rgl or threejs. The threejs will create a htmlwidgets. If 'none' is set, a list of object will be returned.
lwd.backbone, lwd.gene, lwd.tension_line, lwd.maxGenomicSigs: Line width for the linker, gene, interaction node circle, the dashed line of interaction edges, the tension line and the maximal reversed genomic signal.
col.backbone, col.backbone_background, col.tension_line, col.coor: Color for the DNA chain, the compact DNA chain, the node circle, the linker, the tension line and the coordinates marker.
reverseGenomicSigs: Plot the genomic signals in reverse values.
alpha.backbone_background: Alpha channel for transparency of backbone background.
coor_mark_interval: The coordinates marker interval. Numeric(1). Set to 0 to turn it off. The default value 1e5 means show coordinates every 0.1M bp.
show_coor: Plot ticks in the line to show the DNA compact tension.
coor_tick_unit: The bps for every ticks. Default is 1K.
label_gene: Show gene symbol or not.
length.arrow: Length of the edges of the arrow head (in inches).
safe_text_force: The loops to avoid the text overlapping.
square: A logical value that controls whether control points for the curve are created city-block fashion or obliquely. See grid.curve.
cluster3Dpoints: A logical value that controls whether cluster the points in 3D. It will be ignored when k=2.
...: Parameters for create3dGenomicSignals.

Value

Coordinates for 2d or a list of threeJsGeometry objects or a htmlwidget.

Examples

obj <- readRDS(system.file("extdata", "4DNFI1UEG1HD.chr21.FLAMINGO.res.rds",
  package = "geomeTriD"
))
feature.gr <- readRDS(system.file("extdata", "4DNFI1UEG1HD.feature.gr.rds",
  package = "geomeTriD"
))
tjg <- view3dStructure(obj,
  k = 3, feature.gr = feature.gr, renderer = "none",
  length.arrow = grid::unit(0.000006, "native")
)