plotMA-methods {geneplotter} | R Documentation

## Generate an MA plot

### Description

Generate a plot of log fold change versus mean expression (MA plot)

### Usage

    ## S4 method for signature 'data.frame'
    plotMA( object, ylim = NULL,
      colNonSig = "gray32", colSig = "red3", colLine = "#ff000080",
      log = "x", cex=0.45, xlab="mean expression", ylab="log fold change", ... )

### Arguments

`object` | A `data.frame` with (at least) three columns, the first containing the mean expression values (for the x-axis), the second the logarithmic fold change (for the-y axis) and the third a logical vector indicating significance (for the colouring of the dots).
`ylim` | The limits for the y-axis. If missing, an attempt is made to choose a sensible value. Dots exceeding the limits will be displayed as triangles at the limits, pointing outwards.
`colNonSig` | colour to use for non-significant data points.
`colSig` | colour to use for significant data points.
`colLine` | colour to use for the horizontal (y=0) line.
`log` | which axis/axes should be logarithmic; will be passed to `plot`.
`cex` | The `cex` parameter for `plot`.
`xlab` | The x-axis label.
`ylab` | The y-axis label.
`...` | Further parameters to be passed through to `plot`.

### Examples

      plotMA(
        data.frame(
          `M` = exp(rexp(1000)),
          `A` = rnorm(1000) -> tmp,
          `isde` = abs(tmp)>2)
      )

[Package geneplotter version 1.60.0 Index]