manyLoopPlots {diffloop} | R Documentation

## Plot several loop regions

### Description

`manyLoopPlots` takes a loops object and creates a time-stamped .pdf file with loop plots (one per page) of all regions specified in the GRanges object.

### Usage

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

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

### Arguments

`x` | loops object
`y` | GRanges object with many regions to be visualized
`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
`maxCounts` | Number of counts associated with thickest loop. Default is largest count in region displayed
`showAnchorWidths` | Display the width of the anchor on the plot? Default = FALSE

### Details

Each plot will show one region sequentially that is supplied in the GRanges object.

### Value

Prints a time stamped .pdf file of top loops

### Examples

    rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
    load(rda)
    jpn.u <- removeSelfLoops(loops.small)
    assoc <- loopAssoc(jpn.u, coef = 2)
    #manyLoopPlots(assoc, regs) #define regs as multiple GRanges

[Package diffloop version 1.12.0 Index]