Plotting and summary of Fasta objects

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Description

Generic functions for plotting and printing the content of a Fasta object.

Usage

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## S3 method for class 'Fasta'
plot(x, y = NULL, col = "tan4", border = "tan4", ...)

## S3 method for class 'Fasta'
summary(object, ...)

Arguments

x

A Fasta object, see below.

y

not used.

col

Color of bar interiors.

border

Color of bar borders.

...

Optional graphical arguments.

object

A Fasta object, see below.

Details

A Fasta object contains biological sequences in the FASTA format. It is a small (S3) extension to a data.frame. It is actually a data.frame containing at least two text columns named Header and Sequence. The Header column contains the headerlines for each sequence, and the Sequence columns the sequences themselves. A Fasta object is typically created by reading a FASTA formatted file into R by readFasta.

A Fasta object can be treated as a data.frame, which makes it quick and easy to search both Header and Sequence for specific regular expressions, sort or re-arrange the ordering of the sequences, extract subsets or add new data to an existing Fasta object.

The plot.Fasta function will display the content of the Fasta object as a bar chart over the lengths of the sequences. The bars are displayed horizontally, and the first sequence is on top, just like in the FASTA file.

The summary.Fasta function will display a text giving the number of sequences and the alphabet, i.e. listing all unique symbols found in the file.

Author(s)

Lars Snipen and Kristian Hovde Liland.

See Also

readFasta, writeFasta.

Examples

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# See the examples in the Help-file for readFasta/writeFasta