plot.MACATevalScoring {macat} | R Documentation

## Plot function for MACATevalScoring objects.

### Description

Function plots scores, 0.025 and 0.975 quantiles of the permuted scores (grey lines), and sliding average score (red line) along the chromosome. Yellow dots highlight regions, in which the smoothed absolute scores exceed the permutation-derived quantile boundaries.

### Usage

    ## S3 method for class 'MACATevalScoring':
    plot(x, output = "x11",
                  HTMLfilename = NULL, mytitle = NULL, new.device = TRUE, ...)

### Arguments

`x` | MACATevalScoring object.
`output` | plot "x11" or create a "html" -file with further information. HTML-page will open automatically.
`HTMLfilename` | HTML-filename, default:`Results<CHOMOSOME>_<CLASS>.html`
`mytitle` | Title of HTML-page, default: “Results of class <CLASS> on chromosome <CHROMOSOME>”
`new.device` | if FALSE: Possibility to plot several plots in one device
`...` | further arguments passed on to generic function `plot`

### Details

One can create a HTML-page on-the-fly if argument output='html'. The HTML-page provides informations about highlighted regions in the plot. Furthermore there are click-able Entrezgene-IDs for further analysis.

### Author(s)

MACAT development team

### See Also

`evalScoring`, `getResults`

### Examples

     # see function 'evalScoring' for an example

[Package macat version 1.18.0 Index]