loopBouquetPlot: plot GInteractions

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 GInteractions

Description

plot graph for GInteractions

Usage

loopBouquetPlot(
  gi,
  range,
  feature.gr,
  atacSig,
  label_region = FALSE,
  show_edges = TRUE,
  show_cluster = TRUE,
  lwd.backbone = 2,
  col.backbone = "gray",
  lwd.maxAtacSig = 8,
  reverseATACSig = TRUE,
  col.backbone_background = "gray70",
  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.
atacSig	The ATAC-seq signals. An object of GRanges with scores or an object of track.
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.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.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.
reverseATACSig	Plot the ATAC-seq signals in reverse values.
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.
method	Plot method. Could be 1 or 2.
doReduce	Reduce the GInteractions or not.
...	Parameter will be passed to layout_with_fr.

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))
loopBouquetPlot(gi, range, feature.gr)

jianhong/trackViewer documentation built on March 17, 2024, 2:16 p.m.