plotFeature {HELP} | R Documentation |
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.
- ...
- other arguments to be passed to
plot . See plot .
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Author(s)
Reid F. Thompson (rthompso@aecom.yu.edu)
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)
[Package
HELP version 1.2.0
Index]