addInteractionAnnotation: Add annotation markers to the figure at a given position

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

Add annotation markers to the figure at a given position

Description

A function to add annotation markers for emphasizing interactions

Usage

addInteractionAnnotation(
  obj,
  idx,
  FUN = grid.polygon,
  panel = c("top", "bottom"),
  ...
)

Arguments

obj	A GInteractions object, GRanges object or numeric vector. For numeric vector, the positive value will generate a line with slope 1 and negative value will generate a line at the position with slope -1.
idx	The layer number of track.
FUN	Function for plot. Available functions are grid.polygon, grid.lines, and grid.text for GInteractions object; grid.lines, and grid.text for GRanges object; FUN is not used for numeric vector.
panel	Plot regions. Available values are "top", "bottom".
...	Parameters will be passed to FUN.

Value

invisible viewport for plot region.

See Also

See Also as addGuideLine, addArrowMark

Examples

library(trackViewer)
library(InteractionSet)
gi <- readRDS(system.file("extdata", "nij.chr6.51120000.53200000.gi.rds",
 package="trackViewer"))
tads <- GInteractions(
GRanges("chr6", 
        IRanges(c(51130001, 51130001, 51450001, 52210001), width = 20000)),
GRanges("chr6", 
        IRanges(c(51530001, 52170001, 52210001, 53210001), width = 20000)))
range <- GRanges("chr6", IRanges(51120000, 53200000))
tr <- gi2track(gi)
viewTracks(trackList(tr), 
           gr=range, autoOptimizeStyle = TRUE)
addInteractionAnnotation(tads, "tr", grid.lines,
 gp=gpar(col = "#E69F00", lwd=3, lty=3))

jianhong/trackViewer documentation built on Dec. 10, 2024, 10:33 a.m.