Package 'geomeTriD' reference manual

Title:	A R/Bioconductor package for interactive 3D plot of epigenetic data or single cell data
Description:	geomeTriD (Three Dimensional Geometry Package) create interactive 3D plots using the GL library with the 'three.js' visualization library (https://threejs.org) or the rgl library. In addition to creating interactive 3D plots, the application also generates simplified models in 2D. These 2D models provide a more straightforward visual representation, making it easier to analyze and interpret the data quickly. This functionality ensures that users have access to both detailed three-dimensional visualizations and more accessible two-dimensional views, catering to various analytical needs.
Authors:	Jianhong Ou [aut, cre]
Maintainer:	Jianhong Ou <[email protected]>
License:	MIT + file LICENSE
Version:	1.1.1
Built:	2024-11-13 03:36:17 UTC
Source:	https://github.com/bioc/geomeTriD

Interactive 3D plot of epigenetic data or single cell data

Description

geomeTriD (Three Dimensional Geometry Package) create interactive 3D plots using the GL library with the 'three.js' visualization library (https://threejs.org) or the rgl library. In addition to creating interactive 3D plots, the application also generates simplified models in 2D. These 2D models provide a more straightforward visual representation, making it easier to analyze and interpret the data quickly. This functionality ensures that users have access to both detailed three-dimensional visualizations and more accessible two-dimensional views, catering to various analytical needs.

Author(s)

Maintainer: Jianhong Ou [email protected] (ORCID)

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
  )
}

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
  )
}

Aligns two sets of genomic with x,y,z

Description

Aligns two sets of points via rotations and translations by Kabsch Algorithm.

Usage

alignCoor(query, subject)
alignCoor(query, subject)

Arguments

query, subject

GRanges objects to alignment.

Value

A GRanges object of query aligned to subject.

Examples

x <- readRDS(system.file("extdata", "4DNFI1UEG1HD.chr21.FLAMINGO.res.rds",
  package = "geomeTriD"
))
res <- alignCoor(x, x)
A <- view3dStructure(x, k = 3, renderer = "none")
B <- view3dStructure(res, k = 3, renderer = "none")
B <- lapply(B, function(.ele) {
  .ele$side <- "right"
  .ele
})
threeJsViewer(c(A, B))
x <- readRDS(system.file("extdata", "4DNFI1UEG1HD.chr21.FLAMINGO.res.rds",
  package = "geomeTriD"
))
res <- alignCoor(x, x)
A <- view3dStructure(x, k = 3, renderer = "none")
B <- view3dStructure(res, k = 3, renderer = "none")
B <- lapply(B, function(.ele) {
  .ele$side <- "right"
  .ele
})
threeJsViewer(c(A, B))

Available Geometries

Description

The Geometries suported by threeJsGeometry class

Usage

availableGeometries
availableGeometries

Format

An object of class character of length 18.

Examples

availableGeometries

availableGeometries

create 3d Geometry by given genomic signals

Description

Create a 3d Geometry by given genomic signals for target 3d positions.

Usage

create3dGenomicSignals(
  GenoSig,
  targetObj,
  signalTransformFun,
  positionTransformFun,
  genomicScoreRange,
  reverseGenomicSigs,
  type = "segment",
  tag,
  name,
  color = c("gray30", "darkred"),
  rotation = c(0, 0, 0),
  ...
)
create3dGenomicSignals(
  GenoSig,
  targetObj,
  signalTransformFun,
  positionTransformFun,
  genomicScoreRange,
  reverseGenomicSigs,
  type = "segment",
  tag,
  name,
  color = c("gray30", "darkred"),
  rotation = c(0, 0, 0),
  ...
)

Arguments

`GenoSig`	The Genomic signals. An object of GRanges, Pairs, or GInteractions with scores or an object of track.
`targetObj`	The GRanges object with mcols x0, y0, z0, x1, y1, and z1
`signalTransformFun`	The transformation function for genomic signals.
`positionTransformFun`	The transformation function for the coordinates. The function must have input as a data.frame with colnames x0, y0, z0, x1, y1, and z1. And it must have output as same dimension data.frame.
`genomicScoreRange`	The genomic signals range.
`reverseGenomicSigs`	Plot the genomic signals in reverse values.
`type`	The Geometry type.See threeJsGeometry
`tag`	The tag used to group geometries.
`name`	The prefix for the name of the geometries.
`color`	The color of the signal. If there is metadata 'color' in GenoSig this parameter will be ignored.
`rotation`	The rotations in the x, y and z axis in radians.
`...`	the parameters for each different type of geometries. If type is 'segments', lwd.maxGenomicSigs (the maximal lwd of the line) is required. If type is 'circle', radius (the radius of the circle) and the maxVal (the value for 2*pi) is required. If type is 'sphere', 'dodecahedron', 'icosahedron', 'octahedron', or 'tetrahedron', radius is required. If type is 'box', 'capsule', 'cylinder', 'cone', or 'torus', if the properties of correspond geometry is not set, they will be set to the transformed score value. If type is 'json', please refer the documentation about BufferGeometryLoader at threejs.org If input 'GenoSig' is an object of Pairs or GInteractions, the type will be set to 'polygon' and topN is used to set how many top events will be plot.

Value

threeJsGeometry objects or NULL

Examples

library(GenomicRanges)
GenoSig <- GRanges("chr1", IRanges(seq(1, 100, by = 10), width = 10),
  score = seq.int(10)
)
pos <- matrix(rnorm(303), ncol = 3)
pos <- cbind(
  x0 = pos[seq.int(100), 1],
  x1 = pos[seq.int(101)[-1], 1],
  y0 = pos[seq.int(100), 2],
  y1 = pos[seq.int(101)[-1], 2],
  z0 = pos[seq.int(100), 3],
  z1 = pos[seq.int(101)[-1], 3]
)
targetObj <- GRanges("chr1", IRanges(seq.int(100), width = 1))
mcols(targetObj) <- pos
ds <- create3dGenomicSignals(GenoSig, targetObj,
  signalTransformFun = function(x) {
    log2(x + 1)
  },
  reverseGenomicSigs = FALSE,
  type = "segment",
  lwd.maxGenomicSigs = 8,
  name = "test",
  tag = "test"
)
threeJsViewer(ds)
library(GenomicRanges)
GenoSig <- GRanges("chr1", IRanges(seq(1, 100, by = 10), width = 10),
  score = seq.int(10)
)
pos <- matrix(rnorm(303), ncol = 3)
pos <- cbind(
  x0 = pos[seq.int(100), 1],
  x1 = pos[seq.int(101)[-1], 1],
  y0 = pos[seq.int(100), 2],
  y1 = pos[seq.int(101)[-1], 2],
  z0 = pos[seq.int(100), 3],
  z1 = pos[seq.int(101)[-1], 3]
)
targetObj <- GRanges("chr1", IRanges(seq.int(100), width = 1))
mcols(targetObj) <- pos
ds <- create3dGenomicSignals(GenoSig, targetObj,
  signalTransformFun = function(x) {
    log2(x + 1)
  },
  reverseGenomicSigs = FALSE,
  type = "segment",
  lwd.maxGenomicSigs = 8,
  name = "test",
  tag = "test"
)
threeJsViewer(ds)

Extract the backbone coordinates from output of mdsPlot

Description

Extract the positions from output of mdsPlot and used as the 'targetObj' for function create3dGenomicSignals

Usage

extractBackbonePositions(v3d_output)
extractBackbonePositions(v3d_output)

Arguments

v3d_output

The output of mdsPlot or view3dStructure for k=3.

Value

An GRanges object with positions of x0, x1, y0, y1, z0 and z1.

Examples

library(GenomicRanges)
gi_nij <- readRDS(system.file("extdata", "nij.chr6.51120000.53200000.gi.rds",
                  package = "geomeTriD"))
range_chr6 <- GRanges("chr6", IRanges(51120000, 53200000))
geos <- mdsPlot(gi_nij, range = range_chr6, k = 3, render = "none")
extractBackbonePositions(geos)
library(GenomicRanges)
gi_nij <- readRDS(system.file("extdata", "nij.chr6.51120000.53200000.gi.rds",
                  package = "geomeTriD"))
range_chr6 <- GRanges("chr6", IRanges(51120000, 53200000))
geos <- mdsPlot(gi_nij, range = range_chr6, k = 3, render = "none")
extractBackbonePositions(geos)

plot GInteractions

Description

plot graph for GInteractions

Usage

loopBouquetPlot(
  gi,
  range,
  feature.gr,
  genomicSigs,
  signalTransformFun = function(x) {
     log2(x + 1)
 },
  label_region = FALSE,
  show_edges = TRUE,
  show_cluster = TRUE,
  lwd.backbone = 2,
  col.backbone = "gray",
  lwd.maxGenomicSigs = 8,
  reverseGenomicSigs = TRUE,
  col.backbone_background = "gray70",
  alpha.backbone_background = 0.5,
  lwd.gene = 2,
  lwd.nodeCircle = 1,
  col.nodeCircle = "#DDDDDD25",
  lwd.edge = 2,
  col.edge = "gray80",
  coor_mark_interval = 1e+05,
  col.coor = "black",
  show_coor = TRUE,
  coor_tick_unit = 1000,
  label_gene = TRUE,
  col.tension_line = "black",
  lwd.tension_line = 1,
  length.arrow = NULL,
  safe_text_force = 3,
  method = 1,
  doReduce = FALSE,
  ...
)
loopBouquetPlot(
  gi,
  range,
  feature.gr,
  genomicSigs,
  signalTransformFun = function(x) {
     log2(x + 1)
 },
  label_region = FALSE,
  show_edges = TRUE,
  show_cluster = TRUE,
  lwd.backbone = 2,
  col.backbone = "gray",
  lwd.maxGenomicSigs = 8,
  reverseGenomicSigs = TRUE,
  col.backbone_background = "gray70",
  alpha.backbone_background = 0.5,
  lwd.gene = 2,
  lwd.nodeCircle = 1,
  col.nodeCircle = "#DDDDDD25",
  lwd.edge = 2,
  col.edge = "gray80",
  coor_mark_interval = 1e+05,
  col.coor = "black",
  show_coor = TRUE,
  coor_tick_unit = 1000,
  label_gene = TRUE,
  col.tension_line = "black",
  lwd.tension_line = 1,
  length.arrow = NULL,
  safe_text_force = 3,
  method = 1,
  doReduce = FALSE,
  ...
)

Arguments

`gi`	An object of GInteractions
`range`	The region to plot. an object of GRanges
`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.
`signalTransformFun`	The transformation function for genomic signals.
`label_region`	Label the region node or not.
`show_edges`	Plot the interaction edges or not.
`show_cluster`	Plot the cluster background or not.
`lwd.backbone`, `lwd.gene`, `lwd.nodeCircle`, `lwd.edge`, `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.nodeCircle`, `col.edge`, `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`	Show coordinates or not.
`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.
`method`	Plot method. Could be 1 or 2.
`doReduce`	Reduce the GInteractions or not.
`...`	Parameter will be passed to layout_with_fr.

Value

A invisible list with the key points of the plot.

Examples

library(InteractionSet)
gi <- readRDS(system.file("extdata", "gi.rds", package = "trackViewer"))
range <- GRanges("chr2", IRanges(234500000, 235000000))
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
feature.gr <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene)
feature.gr <- subsetByOverlaps(feature.gr, range(regions(gi)))
symbols <- mget(feature.gr$gene_id, org.Hs.egSYMBOL, ifnotfound = NA)
feature.gr$label[lengths(symbols) == 1] <- unlist(symbols[lengths(symbols) == 1])
feature.gr$col <- sample(1:7, length(feature.gr), replace = TRUE)
feature.gr$type <- sample(c("cRE", "gene"),
  length(feature.gr),
  replace = TRUE,
  prob = c(0.1, 0.9)
)
feature.gr$pch <- rep(NA, length(feature.gr))
feature.gr$pch[feature.gr$type == "cRE"] <- 11
loopBouquetPlot(gi, range, feature.gr)
library(InteractionSet)
gi <- readRDS(system.file("extdata", "gi.rds", package = "trackViewer"))
range <- GRanges("chr2", IRanges(234500000, 235000000))
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
feature.gr <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene)
feature.gr <- subsetByOverlaps(feature.gr, range(regions(gi)))
symbols <- mget(feature.gr$gene_id, org.Hs.egSYMBOL, ifnotfound = NA)
feature.gr$label[lengths(symbols) == 1] <- unlist(symbols[lengths(symbols) == 1])
feature.gr$col <- sample(1:7, length(feature.gr), replace = TRUE)
feature.gr$type <- sample(c("cRE", "gene"),
  length(feature.gr),
  replace = TRUE,
  prob = c(0.1, 0.9)
)
feature.gr$pch <- rep(NA, length(feature.gr))
feature.gr$pch[feature.gr$type == "cRE"] <- 11
loopBouquetPlot(gi, range, feature.gr)

Plot genomic interactions by multi-dimensional scaling plot

Description

This function will convert the interactions scores into a distance matrix and then plot the matrix by multi-dimensional scaling plot.

Usage

mdsPlot(
  gi,
  range,
  feature.gr,
  k = 2,
  genomicSigs,
  signalTransformFun = function(x) {
     log2(x + 1)
 },
  lwd.backbone = 2,
  col.backbone = "gray",
  lwd.maxGenomicSigs = 8,
  reverseGenomicSigs = TRUE,
  col.backbone_background = if (k == 2) "gray70" else c("white", "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 = NULL,
  safe_text_force = 3,
  square = TRUE,
  renderer = c("rgl", "threejs", "none", "granges"),
  ...
)
mdsPlot(
  gi,
  range,
  feature.gr,
  k = 2,
  genomicSigs,
  signalTransformFun = function(x) {
     log2(x + 1)
 },
  lwd.backbone = 2,
  col.backbone = "gray",
  lwd.maxGenomicSigs = 8,
  reverseGenomicSigs = TRUE,
  col.backbone_background = if (k == 2) "gray70" else c("white", "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 = NULL,
  safe_text_force = 3,
  square = TRUE,
  renderer = c("rgl", "threejs", "none", "granges"),
  ...
)

Arguments

`gi`	An object of GInteractions
`range`	The region to plot. an object of GRanges
`feature.gr`	The annotation features to be added. An object of GRanges.
`k`	The dimension of plot. 2: 2d, 3: 3d.
`genomicSigs`	The genomic signals. An object of GRanges with scores or an object of track.
`signalTransformFun`	The transformation function for genomic signals.
`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.
`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. If 'granges' is set, A GRanges with coordinates will be returned.
`...`	Parameter will be passed to isoMDS.

Value

Coordinates for 2d or 3d.

Examples

library(InteractionSet)
gi <- readRDS(system.file("extdata", "nij.chr6.51120000.53200000.gi.rds",
  package = "geomeTriD"
))
range <- GRanges("chr6", IRanges(51120000, 53200000))
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
feature.gr <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene)
feature.gr <- subsetByOverlaps(feature.gr, range(regions(gi)))
symbols <- mget(feature.gr$gene_id, org.Hs.egSYMBOL, ifnotfound = NA)
feature.gr$label[lengths(symbols) == 1] <- unlist(symbols[lengths(symbols) == 1])
feature.gr$col <- sample(1:7, length(feature.gr), replace = TRUE)
feature.gr$type <- sample(c("cRE", "gene"),
  length(feature.gr),
  replace = TRUE,
  prob = c(0.1, 0.9)
)
mdsPlot(gi, range, feature.gr)
library(InteractionSet)
gi <- readRDS(system.file("extdata", "nij.chr6.51120000.53200000.gi.rds",
  package = "geomeTriD"
))
range <- GRanges("chr6", IRanges(51120000, 53200000))
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
feature.gr <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene)
feature.gr <- subsetByOverlaps(feature.gr, range(regions(gi)))
symbols <- mget(feature.gr$gene_id, org.Hs.egSYMBOL, ifnotfound = NA)
feature.gr$label[lengths(symbols) == 1] <- unlist(symbols[lengths(symbols) == 1])
feature.gr$col <- sample(1:7, length(feature.gr), replace = TRUE)
feature.gr$type <- sample(c("cRE", "gene"),
  length(feature.gr),
  replace = TRUE,
  prob = c(0.1, 0.9)
)
mdsPlot(gi, range, feature.gr)

rgl Viewer View the 3d structure by rgl.

Description

rgl Viewer View the 3d structure by rgl.

Usage

rglViewer(..., background = "gray")
rglViewer(..., background = "gray")

Arguments

`...`	objects of threeJsGeometry.
`background`	background of the main camera.

Value

MULL

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")
)
rglViewer(tjg, background = 'white')
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")
)
rglViewer(tjg, background = 'white')

Calculate the smoothed curve for input GRanges

Description

This function will do smooth for given resolution (tile) for inputs and it is important step to prepare the inputs for create3dGenomicSignals and view3dStructure.

Usage

smooth3dPoints(obj, resolution = 30, ...)
smooth3dPoints(obj, resolution = 30, ...)

Arguments

`obj`	GRanges object with mcols x, y, and z
`resolution`	number of points at which to evaluate the smooth curve.
`...`	parameters passed to splinefun

Value

GRanges object with smoothed points of x0, y0, z0, x1, y1, and z1.

Examples

library(GenomicRanges)
obj <- GRanges("1", IRanges(seq.int(5) * 10, width = 10),
  x = seq.int(5), y = seq.int(5), z = seq.int(5)
)
smooth3dPoints(obj, 5)

library(GenomicRanges)
obj <- GRanges("1", IRanges(seq.int(5) * 10, width = 10),
  x = seq.int(5), y = seq.int(5), z = seq.int(5)
)
smooth3dPoints(obj, 5)

Class `"threeJsGeometry"`

Description

An object of class "threeJsGeometry" represents 'three.js' geometry.

Usage

threeJsGeometry(...)

## S4 method for signature 'threeJsGeometry'
x$name

## S4 replacement method for signature 'threeJsGeometry'
x$name <- value

## S4 method for signature 'threeJsGeometry'
show(object)
threeJsGeometry(...)

## S4 method for signature 'threeJsGeometry'
x$name

## S4 replacement method for signature 'threeJsGeometry'
x$name <- value

## S4 method for signature 'threeJsGeometry'
show(object)

Arguments

`...`	Each argument in ... becomes an slot in the new threeJsGeometry.
`x`	an object of threeJsGeometry
`name`	slot name of threeJsGeometry
`value`	value to be assigned
`object`	an object of threeJsGeometry

Slots

x,y,z: "numeric", specify the x, y, and z coordinates.
rotation: "numeric", specify the rotations in the x, y and z axis in radians.
colors: "character", the colors for each geometry.
type: "charater", the type of the geometry. See availableGeometries.
side: 'character', the side for side by side plot in threeJsViewer.
layer: 'character', the two layer plot in threeJsViewer.
tag: 'character', the tag used to group geometries.
properties: A "list", the properties to control the geometry.

Examples

tjg <- threeJsGeometry()

tjg <- threeJsGeometry()

threeJs Viewer The htmlwidgets viewer for threeJs.

Description

threeJs Viewer The htmlwidgets viewer for threeJs.

Usage

threeJsViewer(
  ...,
  background = c("#33333388", "#444444DD", "#444444DD", "#33333388"),
  maxRadius = 1,
  maxLineWidth = 50,
  title = NULL,
  width = NULL,
  height = NULL
)
threeJsViewer(
  ...,
  background = c("#33333388", "#444444DD", "#444444DD", "#33333388"),
  maxRadius = 1,
  maxLineWidth = 50,
  title = NULL,
  width = NULL,
  height = NULL
)

Arguments

`...`	objects of threeJsGeometry.
`background`	background of the main camera (left and right).
`maxRadius`	max value of the controls for radius.
`maxLineWidth`	max value of the controls for line width.
`title`	the titles of the plot.
`width`, `height`	width and height of the widgets.

Value

A htmlwidgets widget.

Examples

library(GenomicRanges)
flamingo <- system.file("extdata", "4DNFI1UEG1HD.chr21.FLAMINGO.res.rds", package = "geomeTriD")
x <- readRDS(flamingo[[1]])
## resize to bigger value to get better init view
mcols(x) <- as.data.frame(mcols(x)) * 1e5
set.seed(1)
line <- threeJsGeometry(
  x = x$x, y = x$y, z = x$z,
  colors = sample(palette(), length(x), replace = TRUE),
  type = "line",
  properties = list(size = 4)
)
sphere <- x[sample.int(length(x), 100)]
sphere <- threeJsGeometry(
  x = sphere$x, y = sphere$y, z = sphere$z,
  colors = "red",
  type = "sphere",
  properties = list(radius = 0.08)
)
torus <- x[sample.int(length(x), 100)]
torus <- threeJsGeometry(
  x = torus$x, y = torus$y, z = torus$z,
  colors = "blue",
  type = "torus",
  properties = list(
    radius = 0.08,
    tube = 0.03
  )
)
cylinder <- x[sample.int(length(x), 100)]
cylinder <- threeJsGeometry(
  x = cylinder$x, y = cylinder$y, z = cylinder$z,
  colors = "green",
  type = "cylinder",
  properties = list(
    "height" = 0.07,
    "radiusTop" = 0.05,
    "radiusBottom" = 0.09
  )
)
labels <- x[sample.int(length(x), 5)]
fontURL <- paste0('https://raw.githubusercontent.com/mrdoob/three.js/refs/',
   'heads/dev/examples/fonts/helvetiker_regular.typeface.json')
labels <- threeJsGeometry(
  x = labels$x, y = labels$y, z = labels$z,
  colors = "black",
  type = "text",
  properties = list(
    "label" = "text",
    "font" = readLines(fontURL),
    "size" = .5,
    "depth" = .1
  )
)
threeJsViewer(line, sphere, torus, cylinder)
library(GenomicRanges)
flamingo <- system.file("extdata", "4DNFI1UEG1HD.chr21.FLAMINGO.res.rds", package = "geomeTriD")
x <- readRDS(flamingo[[1]])
## resize to bigger value to get better init view
mcols(x) <- as.data.frame(mcols(x)) * 1e5
set.seed(1)
line <- threeJsGeometry(
  x = x$x, y = x$y, z = x$z,
  colors = sample(palette(), length(x), replace = TRUE),
  type = "line",
  properties = list(size = 4)
)
sphere <- x[sample.int(length(x), 100)]
sphere <- threeJsGeometry(
  x = sphere$x, y = sphere$y, z = sphere$z,
  colors = "red",
  type = "sphere",
  properties = list(radius = 0.08)
)
torus <- x[sample.int(length(x), 100)]
torus <- threeJsGeometry(
  x = torus$x, y = torus$y, z = torus$z,
  colors = "blue",
  type = "torus",
  properties = list(
    radius = 0.08,
    tube = 0.03
  )
)
cylinder <- x[sample.int(length(x), 100)]
cylinder <- threeJsGeometry(
  x = cylinder$x, y = cylinder$y, z = cylinder$z,
  colors = "green",
  type = "cylinder",
  properties = list(
    "height" = 0.07,
    "radiusTop" = 0.05,
    "radiusBottom" = 0.09
  )
)
labels <- x[sample.int(length(x), 5)]
fontURL <- paste0('https://raw.githubusercontent.com/mrdoob/three.js/refs/',
   'heads/dev/examples/fonts/helvetiker_regular.typeface.json')
labels <- threeJsGeometry(
  x = labels$x, y = labels$y, z = labels$z,
  colors = "black",
  type = "text",
  properties = list(
    "label" = "text",
    "font" = readLines(fontURL),
    "size" = .5,
    "depth" = .1
  )
)
threeJsViewer(line, sphere, torus, cylinder)

Shiny bindings for threeJsViewer

Description

Output and render functions for using threeJsViewer within Shiny applications and interactive Rmd documents.

Usage

threejsOutput(outputId, width = "100%", height = "600px")

renderthreeJsViewer(expr, env = parent.frame(), quoted = FALSE)
threejsOutput(outputId, width = "100%", height = "600px")

renderthreeJsViewer(expr, env = parent.frame(), quoted = FALSE)

Arguments

`outputId`	output variable to read from
`width`, `height`	Must be a valid CSS unit (like `'100%'`, `'600px'`, `'auto'`) or a number, which will be coerced to a string and have `'px'` appended.
`expr`	An expression that generates a threeJsViewer
`env`	The environment in which to evaluate `expr`.
`quoted`	Is `expr` a quoted expression (with `quote()`)? This is useful if you want to save an expression in a variable.

Value

An output or render function that enables the use of the threeJsViewer widget.

Examples

if (interactive()) {
  library(GenomicRanges)
  flamingo <- system.file("extdata", "4DNFI1UEG1HD.chr21.FLAMINGO.res.rds", package = "geomeTriD")
  x <- readRDS(flamingo[[1]])
  ## resize to bigger value to get better init view
  mcols(x) <- as.data.frame(mcols(x)) * 1e5
  line <- threeJsGeometry(
    x = x$x, y = x$y, z = x$z,
    colors = sample(palette(), length(x), replace = TRUE),
    type = "line",
    properties = list(size = 4)
  )
  library(shiny)
  runApp(list(
    ui = bootstrapPage(
      threejsOutput("plot")
    ),
    server = function(input, output) {
      output$plot <- renderthreeJsViewer({
        threeJsViewer(line)
      })
    }
  ))
}
if (interactive()) {
  library(GenomicRanges)
  flamingo <- system.file("extdata", "4DNFI1UEG1HD.chr21.FLAMINGO.res.rds", package = "geomeTriD")
  x <- readRDS(flamingo[[1]])
  ## resize to bigger value to get better init view
  mcols(x) <- as.data.frame(mcols(x)) * 1e5
  line <- threeJsGeometry(
    x = x$x, y = x$y, z = x$z,
    colors = sample(palette(), length(x), replace = TRUE),
    type = "line",
    properties = list(size = 4)
  )
  library(shiny)
  runApp(list(
    ui = bootstrapPage(
      threejsOutput("plot")
    ),
    server = function(input, output) {
      output$plot <- renderthreeJsViewer({
        threeJsViewer(line)
      })
    }
  ))
}

Plot cell xyz data in 2d or 3d

Description

Plot cell xyz data with grid or rgl package.

Usage

view3dCells(
  cells,
  x,
  y,
  z,
  color = "blue",
  colorFun = function(x, pal = seq.int(8)) {
     if (is.character(x)) 
         x <-
    as.numeric(factor(x))
     limits <- range(x)
     pal[findInterval(x, seq(limits[1],
    limits[2], length.out = length(pal) + 1), all.inside = TRUE)]
 },
  shape = "sphere",
  radius = 0.1,
  tag = "cell",
  renderer = c("rgl", "threejs", "none"),
  ...
)
view3dCells(
  cells,
  x,
  y,
  z,
  color = "blue",
  colorFun = function(x, pal = seq.int(8)) {
     if (is.character(x)) 
         x <-
    as.numeric(factor(x))
     limits <- range(x)
     pal[findInterval(x, seq(limits[1],
    limits[2], length.out = length(pal) + 1), all.inside = TRUE)]
 },
  shape = "sphere",
  radius = 0.1,
  tag = "cell",
  renderer = c("rgl", "threejs", "none"),
  ...
)

Arguments

`cells`	A data.frame.
`x`, `y`, `z`	Column names of x, y, z.
`color`, `shape`, `radius`	The column names for color, shape, radius or the value(length=1) of them.
`colorFun`	The function to map values into colors.
`tag`	The tag for controler.
`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.
`...`	Not used.

Value

A list of threeJsGeometry objects or a htmlwidget.

Examples

cells <- readRDS(system.file("extdata", "pbmc_small.3d.rds",
  package = "geomeTriD"
))
view3dCells(cells,
  x = "umap_1", y = "umap_2", z = "umap_3",
  color = "nCount_RNA",
  renderer = "threejs"
)
cells <- readRDS(system.file("extdata", "pbmc_small.3d.rds",
  package = "geomeTriD"
))
view3dCells(cells,
  x = "umap_1", y = "umap_2", z = "umap_3",
  color = "nCount_RNA",
  renderer = "threejs"
)

Plot GRanges xyz data in 2d or 3d

Description

Plot GRanges xyz data with grid or rgl package.

Usage

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

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.
`...`	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")
)
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")
)

Package 'geomeTriD'

Help Index

Interactive 3D plot of epigenetic data or single cell data

Description

Author(s)

See Also

Examples

Aligns two sets of genomic with x,y,z

Description

Usage

Arguments

Value

Examples

Available Geometries

Description

Usage

Format

Examples

create 3d Geometry by given genomic signals

Description

Usage

Arguments

Value

Examples

Extract the backbone coordinates from output of mdsPlot

Description

Usage

Arguments

Value

Examples

plot GInteractions

Description

Usage

Arguments

Value

Examples

Plot genomic interactions by multi-dimensional scaling plot

Description

Usage

Arguments

Value

Examples

rgl Viewer View the 3d structure by rgl.

Description

Usage

Arguments

Value

Examples

Calculate the smoothed curve for input GRanges

Description

Usage

Arguments

Value

Examples

Class "threeJsGeometry"

Description

Usage

Arguments

Slots

Examples

threeJs Viewer The htmlwidgets viewer for threeJs.

Description

Usage

Arguments

Value

Examples

Shiny bindings for threeJsViewer

Description

Usage

Arguments

Value

Examples

Plot cell xyz data in 2d or 3d

Description

Usage

Arguments

Value

Examples

Plot GRanges xyz data in 2d or 3d

Description

Class `"threeJsGeometry"`