plotGenoGAM: The pot function for a GenoGAM object

Description Usage Arguments Value Author(s)

View source: R/plotting.R

Description

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

Usage

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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 [email protected]


GenoGAM documentation built on Dec. 7, 2018, 6 p.m.