plotGenoGAM {GenoGAM} | R Documentation

## The pot function for a GenoGAM object

### Description

This functions plots the fit of a given region and optionally the read counts from the GenoGAMDataSet object

### Usage

    plotGenoGAM(x, ggd = NULL, ranges = NULL, seqnames = NULL,
      start = NULL, end = NULL, scale = TRUE, cap = TRUE,
      log = FALSE, ...)

### Arguments

`x` | A `GenoGAM` object
`ggd` | A `GenoGAMDataSet` object to plot raw counts
`ranges` | A `GRanges` object specifying a particular region
`seqnames` | A chromosome name. Together with start and end it is an alternative way ob selecting a region
`start` | The start of a region
`end` | The end of a region
`scale` | Logical, should all tracks be scaled to the same y-axis?
`cap` | If FALSE deactivates the cap that prevents to accidentaly plot a too larger area. The default cap is 1Mbp.
`log` | Should log values be plotted on the y-axis
`...` | Additional parameters that will be passed to the basic plot routine

### Value

A plot of all tracks either using the ggplot2 or the base R framework

### Author(s)

Georg Stricker georg.stricker@in.tum.de

[Package GenoGAM version 2.10.0 Index]