HELP (version 1.30.0)

plotFeature: Plot feature versus two-color intensity

Description

Graphical display of featureData (ex: fragment size) versus two-color signal intensity data

Usage

plotFeature(x, y, ...)

Arguments

x

matrix of numerical data to be plotted, with two columns (one for each signal channel). x can also be of class "ExpressionSet".

y

an additional vector of numerical data to be used for feature. If y is missing, the function will attempt to fill a value from featureData in x.

...

Arguments to be passed to methods (see plotFeature-methods):

element.x

which element of AssayData to use (for signal channel 1) for a given ExpressionSet input (default is "exprs")

element.y

which element of AssayData to use (for signal channel 2) for a given ExpressionSet input (default is "exprs2")

sample

which element of sampleNames to use as data (default is 1). Can be a character matching a sample name or simply an integer indicating which sample to choose.

feature

which element of featureData to use as plotting feature (default is 1). Can be a character matching varLabel or simply an integer indicating which feature to choose.

feature.random

which element of featureData to use to identify random probes (default is "TYPE"). Can be a character matching varLabel or simply an integer indicating which feature to choose.

which.random

an integer vector specifying which rows of data correspond to random probes. if NULL (default), the function will attempt to identify random probes using featureData.

random.flag

a character specifying the label for random probes in feature.random from featureData. Default is "RAND".

na.rm

logical; if TRUE (default), missing values are removed from x. If FALSE any missing values cause an error.

limit

numerical input specifying the maximum number of points to plot (default is 10,000). if NULL, all points will be used.

cutoff

a numerical input specifying the value below which signal intensities from channel 1 can be considered "failed" probes. If NULL (default), the function will attempt to calculate a cutoff from random probe information.

cutoff2

a numerical input specifying the value below which signal intensities from channel 2 can be considered "failed" probes. If NULL (default), the function will attempt to calculate a cutoff from random probe information.

main

an overall title for the plot: see title.

xlab

a title for the x axis (default is "Fragment size (bp)"): see title.

ylab

a title for the y axis for signal channel 1 (default is "log(MspI)"): see title.

ylab2

a title for the y axis for signal channel 2 (default is "log(HpaII)"): see title.

cex

numerical value (default is 0.2) giving the amount by which plotting text and symbols should be scaled relative to the default.

\dots

other arguments to be passed to plot. See plot.

See Also

plotFeature-methods

Examples

#demo(pipeline,package="HELP")

msp1 <- sample(8000:16000/1000, size=1000)
msp1 <- msp1[order(msp1)]
hpa2 <- sample(8000:16000/1000, size=1000)
hpa2 <- hpa2[order(hpa2)]
size <- sample((1:1000)*1.8+200, size=1000)
rand <- which.min(abs(msp1-quantile(msp1, 0.25)))
plotFeature(cbind(msp1, hpa2), size, which.random=(rand-20):(rand+20), main="Random")

#rm(msp1, hpa2, size, rand)