rfamSecondaryStructureXMLSVG: Get an SVG file with a secondary structure representation of...

In rfaRm: An R interface to the Rfam database

Description

Gets a string corresponding to an SVG file (XML format) with a representation of the secondary structure of the Rfam family, which can be read by rsvg or magick. If a filename is provided, the SVG file will also be written to the specified path.

Usage

rfamSecondaryStructureXMLSVG(rfamFamily, filename=NULL, plotType="norm")

Arguments

rfamFamily	string with an Rfam family accession or ID for which a SVG file with a representation of the secondary structure should be retrieved.
filename	string indicating a path to which the SVG graphics should be written. In the default behaviour, filename=NULL, the SVG will not be written to any file, and instead will only be returned as a character string, which can be directly read by R packages such as rsvg and magick.
plotType	string indicating the desired type of secondary structure diagram. Can be one of "cons", "fcbp", "cov", "ent", "maxcm", "norm", "rchie", "rscape" or "rscape-cyk". For a description of each type of diagram, see https://docs.rfam.org/en/latest/api.html#secondary-structure-images.

Value

A string with the contents of a SVG file (XML format) with the representation of a secondary structure diagram of the Rfam family. The string can be directly read by rsvg or magick. If a filename is provided, the SVG file will also be written to the specified path.

References

Ioanna Kalvari, Joanna Argasinska, Natalia Quinones-Olvera, Eric P Nawrocki, Elena Rivas, Sean R Eddy, Alex Bateman, Robert D Finn, Anton I Petrov, Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families, Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D335–D342, https://doi.org/10.1093/nar/gkx1038

https://docs.rfam.org/en/latest/api.html

Examples

# Get a SVG representing a normal secondary structure diagram of the Rfam family
# with ID "FMN"

rfamSecondaryStructureXMLSVG("FMN")

# Get a SVG representing a basepair conservation secondary structure diagram
# for the Rfam family with accession "RF00174", and save it to a file

rfamSecondaryStructureXMLSVG("RF00174", filename="RF00174bpcons.svg", plotType="fcbp")

rfaRm documentation built on March 16, 2021, 6:01 p.m.