R: S3 method for class 'gmdm'

plot.gmdm {GMD} | R Documentation

## S3 method for class ‘gmdm’

### Description

S3 method for class `gmdm`

### Usage

    ## S3 method for class 'gmdm'
    plot(x, labels, colors, type = NULL, main, ylab = "Fraction",
      xlab = "Position", label.length.max = 8, label.line.max = 3,
      cex.text = 1, cex.tickmark = 0.75, if.plot.new = TRUE, ...)

### Arguments

`x` | an object of class `gmdm`.
`labels` | a string vector of the same length as `x$data`, giving the names of the numeric vectors in `x$data`.
`colors` | the colors of the discrete distributions; the default is "Dark2" colors in ColorBrewer palettes if not specified.
`type` | type of plot, as in `help("plot", package="graphics")`.
`main` | an overall title for the plot. See `help("title", package="graphics")`; the default title is used if not specified.
`ylab` | a title for the y axis. See `help("title", package="graphics")`.
`xlab` | a title for the x axis. See `help("title", package="graphics")`.
`label.length.max` | numeric, giving the maximum string width allowed in diagonal labels.
`label.line.max` | numeric, giving the maximum number of lines allowed in diagonal labels.
`cex.text` | a numerical value giving the amount by which plot text should be magnified relative to the default.
`cex.tickmark` | a numerical value giving the amount by which tickmarks should be magnified relative to the default.
`if.plot.new` | logical, indicating whether to start a new plot device.
`...` | arguments to be passed to methods, see `gmdp`.

### Details

S3 method for class `gmdm`

### References

See `help(GMD)`

### See Also

`gmdm`, `gmdp`

### Examples

    ## ------------------------------------------------------------------------
    ## Example1: CAGE
    ## ------------------------------------------------------------------------
    require("GMD") # load library
    data(cage)     # load data

    ## construct a distance matrix and visualize it
    short.labels <- gsub("(.+) \\(.+","\\1",names(cage)) # get short labels
    x <- gmdm(cage[1:6],labels=short.labels[1:6])
    plot(x)

    ## Not run:
    ## ------------------------------------------------------------------------
    ## Example2: ChIP-seq
    ## ------------------------------------------------------------------------
    data(chipseq_mES)   # load data
    data(chipseq_hCD4T) # load data

    ## pairwise distance and alignment based on GMD metric
    plot(gmdm(chipseq_mES,sliding=FALSE))

    ## clustering on spatial distributions of histone modifications
    x <- gmdm(chipseq_hCD4T,sliding=FALSE,resolution=10)
    heatmap.3(x,revC=TRUE)

    ## End(Not run)

[Package GMD version 0.3.3 Index]