mdsPlot: Plot genomic interactions by multi-dimensional scaling plot

In jianhong/trackViewer: A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data

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,
  atacSig,
  lwd.backbone = 2,
  col.backbone = "gray",
  lwd.maxAtacSig = 8,
  reverseATACSig = TRUE,
  col.backbone_background = "gray70",
  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,
  ...
)

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.
atacSig	The ATAC-seq signals. An object of GRanges with scores or an object of track.
lwd.backbone, lwd.gene, lwd.tension_line, lwd.maxAtacSig	Line width for the linker, gene, interaction node circle, the dashed line of interaction edges, the tension line and the maximal reversed ATAC 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.
reverseATACSig	Plot the ATAC-seq 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.
...	Parameter will be passed to isoMDS.

Value

Coordinates for 2d.

Examples

library(InteractionSet) 
gi <- readRDS(system.file("extdata", "nij.chr6.51120000.53200000.gi.rds",
 package="trackViewer"))
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)

jianhong/trackViewer documentation built on June 23, 2024, 7:18 p.m.