loopPlot: Visualize looping

In aryeelab/diffloop: Identifying differential DNA loops from chromatin topology data

Description

loopPlot takes a loops object and a GRanges objectand shows all loops in region (where both anchors are present)

Usage

loopPlot(x, y, organism = "h", geneinfo = "NA", colorLoops = TRUE,
  cache = TRUE, showAnchorWidths = FALSE, maxCounts = -1)

## S4 method for signature 'loops,GRanges'
loopPlot(x, y, organism = "h", geneinfo = "NA",
  colorLoops = TRUE, cache = TRUE, showAnchorWidths = FALSE,
  maxCounts = -1)

Arguments

x	A loops object
y	A GRanges object containing region of interest
organism	'h' for human or 'm' for mouse supported
geneinfo	A data.frame manually specifying annotation (see Examples)
colorLoops	Differentiates loops based on loop.type in loops object
cache	logic variable (default = TRUE) to use gene annotation from July.2015 freeze
showAnchorWidths	Display the width of the anchor on the plot? Default = FALSE
maxCounts	Number of counts associated with thickest loop. Default is largest count in region displayed

Details

Basic plot function shows the looping in each sample. The intensity of the color is proportional to the number of counts observed for the particular loop relative to the other loops in the entire plot. If colorLoops is specified at TRUE, then the x object must be loops and it must have a loop.type column which can be generated from the annotateLoops function. Blue loops are CTCF loops; black are none; red are enhancer-promoter loops; orange are promoter-promoter loops; and purple are enhancer-enhancer loops. Plots use hg19 and mm9 annotation by default.

Value

A plot object

Examples

# Print loops in region chr1:36000000-36300000
library(GenomicRanges)
rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
load(rda)
regA <- GRanges(c('1'),IRanges(start=c(36000000),end=c(36300000)))
plot1 <- loopPlot(loops.small, regA)
#Example of \code{geneinfo} table
geneinfo <- data.frame(1,359345,359681,'RP5-8572K21.15','.',-1)
names(geneinfo) <- c('chrom','start','stop','gene','strand')

aryeelab/diffloop documentation built on May 12, 2019, 3:42 a.m.