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. \dots other arguments to be passed to `plot`. See `plot`.

### 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 1.48.0 Index]