rfamSecondaryStructurePlot: Generate a diagram of the secondary structure of an Rfam...

In rfaRm: An R interface to the Rfam database

Description

Plots a diagram of the specified type of the secondary structure of an Rfam family. If a filename is provided, the diagram will be saved to the specified path.

Usage

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

Arguments

rfamFamily	string with an Rfam family accession or ID for which the secondary structure should be plotted.
filename	string indicating a path to which the plotted diagram should be written. In the default behaviour, filename=NULL, the diagram will not be saved into any file, and instead will only be plotted on R's graphics display. Must be a file type supported by magick, such as PNG, JPEG, GIF, RGB or RGBA.
plotType	string indicating the desired type of secondary structure diagram. Can be one of "cons", "fcbp", "cov", "ent", "maxcm", "norm" (default), "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 magick image object with the requested diagram. If a filename was specified, the diagram plot will also be saved 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

# Plot a normal secondary structure diagram of the Rfam family with ID "FMN"

rfamSecondaryStructurePlot("FMN")

# Save a basepair conservation secondary structure diagram of the Rfam family
# with accession "RF00174" as a PNG file.

rfamSecondaryStructurePlot("RF00174", filename="RF00174bpcons.png", plotType="fcbp")

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