plotReads {girafe} | R Documentation

## Function to plot aligned reads along the chromosome

### Description

Function to plot aligned reads along the chromosome

### Usage

    plotReads(dat, ylim, strand = "plus", vpr, sampleColor = NULL,
       zeroLine = FALSE, main, pointSize = unit(1, "mm"),
       cexAxisLabel = 1, cexAxis = 1, ylab, ...)

### Arguments

`dat` | a list with arguments x.start integer; the genome start coordinates of the data to visualise x.end integer; the genome end coordinates of the data to visualise y numeric; the levels of the data to visualise flag numeric; specifies the category of each value, e.g. marks which data values belong to unique read alignments and which not
`ylim` | y-axis limits of the plotting window
`strand` | string; which of the two strands is plotted
`vpr` | which viewport to use for this plot
`sampleColor` | which colour to use for the data
`zeroLine` | logical; should a line at y=0 be drawn?
`main` | string; main title for the plot
`pointSize` | width of each dot/bar
`cexAxisLabel` | numeric; expansion factor for the axis labels
`cexAxis` | numeric; expansion factor for the axis labels
`ylab` | y-axis label
`...` | further arguments passed on to the more primitive plotting functions that are used

### Details

This function is used inside the plotting method for objects of class `AlignedGenomeIntervals`.

### Value

returns `Null`; called for plotting single reads inside the function `plotAligned`

### Author(s)

Joern Toedling

[Package girafe version 1.42.0 Index]