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`.

### 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 1.0.0 Index]