plotBaits: Plot Baits
In Chicago: CHiCAGO: Capture Hi-C Analysis of Genomic Organization

Description Usage Arguments Value Author(s) Examples

Plot the read counts around baits.

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, ...)

`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`

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

Mikhail Spivakov, Jonathan Cairns, Paula Freire Pritchett

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)