plotBaits {Chicago} | R Documentation

## Plot Baits

### Description

Plot the read counts around baits.

### Usage

    plotBaits(cd, pcol = "score", Ncol = "N", n = 16, baits = NULL,
          plotBaitNames = TRUE, plotBprof = FALSE, plevel1 = 5, plevel2 = 3,
          outfile = NULL, removeBait2bait = TRUE, width = 20, height = 20,
          maxD = 1e6, bgCol = "black", lev2Col = "blue", lev1Col = "red",
          bgPch = 1, lev1Pch = 20, lev2Pch = 20, ...)

### Arguments

`cd` | A `chicagoData` object.
`pcol` | The name of the column that contains the score.
`Ncol` | The name of the column that contains counts.
`n` | The number of baits to plot (ignored if `baits` is specified).
`baits` | The IDs of the baits to plot.
`plotBaitNames` | If `TRUE`, the names of the baits, rather than their IDs, will appear in the plot.
`plotBprof` | If `TRUE`, display a line representing the expected Brownian noise at each distance.
`plevel1, plevel2` | Thresholds used on the `pcol` column. `plevel1` should be the more stringent threshold.
`outfile` | If `NULL`, output to current plotting device. Otherwise, this specifies a pdf file to write to.
`removeBait2bait` | If `TRUE`, bait-to-bait interactions are not plotted.
`width, height` | Passed through to `pdf`
`maxD` | The maximum (linear) distance each side of the bait to plot (NULL to include the whole chromosome).
`bgCol, lev1Col, lev2Col` | Colours to be used for background points, and for the two stringency levels defined by `plevel1` and `plevel2`, respectively.
`bgPch, lev1Pch, lev2Pch` | Plotting character for background points, and for points exceeding the two stringency levels defined by `plevel1` and `plevel2`, respectively. Specified as per `pch` in `points`.
`...` | Additional arguments passed to `plot`

### Value

Vector of the baitIDs plotted (useful if baitIDs were sampled randomly).

### Author(s)

Mikhail Spivakov, Jonathan Cairns, Paula Freire Pritchett

### Examples

    data(cdUnitTest)

    ##modifications to cdUnitTest, ensuring it uses correct design directory
    designDir <- file.path(system.file("extdata", package="Chicago"), "unitTestDesign")
    cdUnitTest <- modifySettings(cd=cdUnitTest, designDir=designDir)

    plotBaits(cdUnitTest)

[Package Chicago version 1.20.0 Index]