Chicago (version 1.0.3)

plotBaits: 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).

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)